>|> 20240920 18:02:38.494 -|- INFO -|- AlignSettings -|- 0x7f44eb41fdc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:02:38.501 -|- INFO -|- CheckPositionalArgs -|- 0x7f44eb41fdc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-7/execution/flnc.bam
>|> 20240920 18:02:38.501 -|- INFO -|- CheckPositionalArgs -|- 0x7f44eb41fdc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:02:38.541 -|- WARN -|- operator() -|- 0x7f44eb41fdc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:02:38.541 -|- INFO -|- Index -|- 0x7f44eb41fdc0|| -|- Start reading/building index
>|> 20240920 18:03:25.158 -|- INFO -|- Index -|- 0x7f44eb41fdc0|| -|- Finished reading/building index
>|> 20240920 18:04:09.432 -|- INFO -|- operator() -|- 0x7f44817fe640|| -|- Merged sorted output from 0 files and 8 in-memory blocks
>|> 20240920 18:04:09.432 -|- INFO -|- Close -|- 0x7f44eb41fdc0|| -|- Generating BAI
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Mapped Reads: 522325
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Alignments: 525673
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Mapped Bases: 765565223
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Mean Gap-Compressed Sequence Identity: 99.6871%
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Max Mapped Read Length: 7467
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Mean Mapped Read Length: 1456.35
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Index Build/Read Time: 49s 126ms 
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Alignment Time: 40s 502ms 
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Sort Merge Time: 1s 249ms 
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- BAI Generation Time: 645ms 106us 
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Run Time: 1m 31s 
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- CPU Time: 40m 35s 
>|> 20240920 18:04:10.077 -|- INFO -|- Runner -|- 0x7f44eb41fdc0|| -|- Peak RSS: 19.853 GB