>|> 20240920 18:26:24.703 -|- INFO -|- AlignSettings -|- 0x7f52d661edc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:26:24.734 -|- INFO -|- CheckPositionalArgs -|- 0x7f52d661edc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-4/execution/flnc.bam
>|> 20240920 18:26:24.734 -|- INFO -|- CheckPositionalArgs -|- 0x7f52d661edc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:26:24.887 -|- WARN -|- operator() -|- 0x7f52d661edc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:26:24.887 -|- INFO -|- Index -|- 0x7f52d661edc0|| -|- Start reading/building index
>|> 20240920 18:27:11.785 -|- INFO -|- Index -|- 0x7f52d661edc0|| -|- Finished reading/building index
>|> 20240920 18:36:03.772 -|- INFO -|- operator() -|- 0x7f52a8fd3640|| -|- Merged sorted output from 24 files and 8 in-memory blocks
>|> 20240920 18:36:03.772 -|- INFO -|- Close -|- 0x7f52d661edc0|| -|- Generating BAI
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Mapped Reads: 6312371
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Alignments: 6373462
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Mapped Bases: 10422090649
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Mean Gap-Compressed Sequence Identity: 99.7704%
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Max Mapped Read Length: 11881
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Mean Mapped Read Length: 1635.23
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Index Build/Read Time: 49s 406ms 
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Alignment Time: 7m 44s 
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Sort Merge Time: 1m 5s 
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- BAI Generation Time: 8s 188ms 
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Run Time: 9m 47s 
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- CPU Time: 7h 2m 
>|> 20240920 18:36:11.961 -|- INFO -|- Runner -|- 0x7f52d661edc0|| -|- Peak RSS: 26.077 GB