>|> 20240920 18:13:56.632 -|- INFO -|- AlignSettings -|- 0x7f1b3fb28dc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:13:56.645 -|- INFO -|- CheckPositionalArgs -|- 0x7f1b3fb28dc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-3/execution/flnc.bam
>|> 20240920 18:13:56.645 -|- INFO -|- CheckPositionalArgs -|- 0x7f1b3fb28dc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:13:56.773 -|- WARN -|- operator() -|- 0x7f1b3fb28dc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:13:56.773 -|- INFO -|- Index -|- 0x7f1b3fb28dc0|| -|- Start reading/building index
>|> 20240920 18:14:43.551 -|- INFO -|- Index -|- 0x7f1b3fb28dc0|| -|- Finished reading/building index
>|> 20240920 18:23:14.047 -|- INFO -|- operator() -|- 0x7f1b09ffd640|| -|- Merged sorted output from 24 files and 8 in-memory blocks
>|> 20240920 18:23:14.047 -|- INFO -|- Close -|- 0x7f1b3fb28dc0|| -|- Generating BAI
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Mapped Reads: 5893949
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Alignments: 5946365
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Mapped Bases: 9877338540
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Mean Gap-Compressed Sequence Identity: 99.7707%
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Max Mapped Read Length: 12742
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Mean Mapped Read Length: 1661.07
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Index Build/Read Time: 49s 294ms 
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Alignment Time: 7m 23s 
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Sort Merge Time: 1m 4s 
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- BAI Generation Time: 7s 690ms 
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Run Time: 9m 25s 
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- CPU Time: 6h 42m 
>|> 20240920 18:23:21.739 -|- INFO -|- Runner -|- 0x7f1b3fb28dc0|| -|- Peak RSS: 26.203 GB