>|> 20240920 18:08:11.715 -|- INFO -|- AlignSettings -|- 0x7f420216ddc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:08:11.726 -|- INFO -|- CheckPositionalArgs -|- 0x7f420216ddc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-2/execution/flnc.bam
>|> 20240920 18:08:11.726 -|- INFO -|- CheckPositionalArgs -|- 0x7f420216ddc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:08:11.851 -|- WARN -|- operator() -|- 0x7f420216ddc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:08:11.851 -|- INFO -|- Index -|- 0x7f420216ddc0|| -|- Start reading/building index
>|> 20240920 18:08:58.428 -|- INFO -|- Index -|- 0x7f420216ddc0|| -|- Finished reading/building index
>|> 20240920 18:12:20.801 -|- INFO -|- operator() -|- 0x7f41c97fb640|| -|- Merged sorted output from 8 files and 8 in-memory blocks
>|> 20240920 18:12:20.801 -|- INFO -|- Close -|- 0x7f420216ddc0|| -|- Generating BAI
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Mapped Reads: 3365512
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Alignments: 3380128
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Mapped Bases: 4639333604
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Mean Gap-Compressed Sequence Identity: 99.4209%
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Max Mapped Read Length: 8228
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Mean Mapped Read Length: 1372.53
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Index Build/Read Time: 49s 94ms 
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Alignment Time: 2m 57s 
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Sort Merge Time: 22s 436ms 
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- BAI Generation Time: 3s 940ms 
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Run Time: 4m 13s 
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- CPU Time: 2h 46m 
>|> 20240920 18:12:24.743 -|- INFO -|- Runner -|- 0x7f420216ddc0|| -|- Peak RSS: 24.644 GB