>|> 20240920 18:39:25.906 -|- INFO -|- AlignSettings -|- 0x7f1704593dc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:39:25.919 -|- INFO -|- CheckPositionalArgs -|- 0x7f1704593dc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-5/execution/flnc.bam
>|> 20240920 18:39:25.919 -|- INFO -|- CheckPositionalArgs -|- 0x7f1704593dc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:39:26.014 -|- WARN -|- operator() -|- 0x7f1704593dc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:39:26.014 -|- INFO -|- Index -|- 0x7f1704593dc0|| -|- Start reading/building index
>|> 20240920 18:40:12.257 -|- INFO -|- Index -|- 0x7f1704593dc0|| -|- Finished reading/building index
>|> 20240920 18:51:00.298 -|- INFO -|- operator() -|- 0x7f16d4fd1640|| -|- Merged sorted output from 32 files and 8 in-memory blocks
>|> 20240920 18:51:00.298 -|- INFO -|- Close -|- 0x7f1704593dc0|| -|- Generating BAI
>|> 20240920 18:51:10.224 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Mapped Reads: 7931362
>|> 20240920 18:51:10.225 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Alignments: 8003940
>|> 20240920 18:51:10.225 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Mapped Bases: 12716812106
>|> 20240920 18:51:10.225 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Mean Gap-Compressed Sequence Identity: 99.7718%
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Max Mapped Read Length: 11243
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Mean Mapped Read Length: 1588.82
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Index Build/Read Time: 48s 729ms 
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Alignment Time: 9m 19s 
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Sort Merge Time: 1m 25s 
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- BAI Generation Time: 9s 921ms 
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Run Time: 11m 44s 
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- CPU Time: 8h 29m 
>|> 20240920 18:51:10.226 -|- INFO -|- Runner -|- 0x7f1704593dc0|| -|- Peak RSS: 26.229 GB