>|> 20240920 18:01:03.515 -|- INFO -|- AlignSettings -|- 0x7f4e082d5dc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:01:03.602 -|- INFO -|- CheckPositionalArgs -|- 0x7f4e082d5dc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-6/execution/flnc.bam
>|> 20240920 18:01:03.602 -|- INFO -|- CheckPositionalArgs -|- 0x7f4e082d5dc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:01:03.885 -|- WARN -|- operator() -|- 0x7f4e082d5dc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:01:03.885 -|- INFO -|- Index -|- 0x7f4e082d5dc0|| -|- Start reading/building index
>|> 20240920 18:01:51.726 -|- INFO -|- Index -|- 0x7f4e082d5dc0|| -|- Finished reading/building index
>|> 20240920 18:02:24.998 -|- INFO -|- operator() -|- 0x7f4dc57f6640|| -|- Merged sorted output from 0 files and 8 in-memory blocks
>|> 20240920 18:02:24.998 -|- INFO -|- Close -|- 0x7f4e082d5dc0|| -|- Generating BAI
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Mapped Reads: 391384
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Alignments: 393691
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Mapped Bases: 562310478
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Mean Gap-Compressed Sequence Identity: 99.6829%
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Max Mapped Read Length: 8557
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Mean Mapped Read Length: 1428.3
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Index Build/Read Time: 50s 332ms 
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Alignment Time: 29s 804ms 
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Sort Merge Time: 963ms 131us 
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- BAI Generation Time: 487ms 780us 
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Run Time: 1m 21s 
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- CPU Time: 30m 23s 
>|> 20240920 18:02:25.486 -|- INFO -|- Runner -|- 0x7f4e082d5dc0|| -|- Peak RSS: 19.626 GB