>|> 20240920 18:24:38.471 -|- INFO -|- AlignSettings -|- 0x7fe98734fdc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:24:38.484 -|- INFO -|- CheckPositionalArgs -|- 0x7fe98734fdc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-10/execution/flnc.bam
>|> 20240920 18:24:38.484 -|- INFO -|- CheckPositionalArgs -|- 0x7fe98734fdc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:24:38.744 -|- WARN -|- operator() -|- 0x7fe98734fdc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:24:38.744 -|- INFO -|- Index -|- 0x7fe98734fdc0|| -|- Start reading/building index
>|> 20240920 18:25:25.111 -|- INFO -|- Index -|- 0x7fe98734fdc0|| -|- Finished reading/building index
>|> 20240920 18:38:32.945 -|- INFO -|- operator() -|- 0x7fe94d7fa640|| -|- Merged sorted output from 32 files and 8 in-memory blocks
>|> 20240920 18:38:32.946 -|- INFO -|- Close -|- 0x7fe98734fdc0|| -|- Generating BAI
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Mapped Reads: 8733760
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Alignments: 8818188
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Mapped Bases: 14678486444
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Mean Gap-Compressed Sequence Identity: 99.7751%
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Max Mapped Read Length: 11257
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Mean Mapped Read Length: 1664.57
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Index Build/Read Time: 48s 859ms 
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Alignment Time: 11m 37s 
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Sort Merge Time: 1m 28s 
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- BAI Generation Time: 11s 451ms 
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Run Time: 14m 5s 
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- CPU Time: 10h 37m 
>|> 20240920 18:38:44.399 -|- INFO -|- Runner -|- 0x7fe98734fdc0|| -|- Peak RSS: 26.360 GB