>|> 20240920 18:06:43.393 -|- INFO -|- AlignSettings -|- 0x7fcb3c059dc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:06:43.407 -|- INFO -|- CheckPositionalArgs -|- 0x7fcb3c059dc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-9/execution/flnc.bam
>|> 20240920 18:06:43.407 -|- INFO -|- CheckPositionalArgs -|- 0x7fcb3c059dc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:06:43.567 -|- WARN -|- operator() -|- 0x7fcb3c059dc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:06:43.567 -|- INFO -|- Index -|- 0x7fcb3c059dc0|| -|- Start reading/building index
>|> 20240920 18:07:29.945 -|- INFO -|- Index -|- 0x7fcb3c059dc0|| -|- Finished reading/building index
>|> 20240920 18:20:16.407 -|- INFO -|- operator() -|- 0x7fcb04ffd640|| -|- Merged sorted output from 32 files and 8 in-memory blocks
>|> 20240920 18:20:16.407 -|- INFO -|- Close -|- 0x7fcb3c059dc0|| -|- Generating BAI
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Mapped Reads: 7069272
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Alignments: 7142785
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Mapped Bases: 14159976047
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Mean Gap-Compressed Sequence Identity: 99.7875%
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Max Mapped Read Length: 11518
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Mean Mapped Read Length: 1982.42
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Index Build/Read Time: 48s 878ms 
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Alignment Time: 11m 15s 
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Sort Merge Time: 1m 27s 
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- BAI Generation Time: 10s 699ms 
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Run Time: 13m 43s 
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- CPU Time: 10h 15m 
>|> 20240920 18:20:27.108 -|- INFO -|- Runner -|- 0x7fcb3c059dc0|| -|- Peak RSS: 26.463 GB