>|> 20240920 17:41:35.853 -|- INFO -|- AlignSettings -|- 0x7f988140edc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 17:41:35.872 -|- INFO -|- CheckPositionalArgs -|- 0x7f988140edc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-0/execution/flnc.bam
>|> 20240920 17:41:35.872 -|- INFO -|- CheckPositionalArgs -|- 0x7f988140edc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 17:41:35.892 -|- WARN -|- operator() -|- 0x7f988140edc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 17:41:35.892 -|- INFO -|- Index -|- 0x7f988140edc0|| -|- Start reading/building index
>|> 20240920 17:42:26.912 -|- INFO -|- Index -|- 0x7f988140edc0|| -|- Finished reading/building index
>|> 20240920 17:47:40.359 -|- INFO -|- operator() -|- 0x7f98557d2640|| -|- Merged sorted output from 16 files and 8 in-memory blocks
>|> 20240920 17:47:40.359 -|- INFO -|- Close -|- 0x7f988140edc0|| -|- Generating BAI
>|> 20240920 17:47:46.487 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Mapped Reads: 4853018
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Alignments: 4874818
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Mapped Bases: 6641472992
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Mean Gap-Compressed Sequence Identity: 99.3886%
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Max Mapped Read Length: 8876
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Mean Mapped Read Length: 1362.4
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Index Build/Read Time: 53s 913ms 
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Alignment Time: 4m 21s 
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Sort Merge Time: 49s 366ms 
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- BAI Generation Time: 6s 127ms 
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Run Time: 6m 10s 
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- CPU Time: 4h 1m 
>|> 20240920 17:47:46.488 -|- INFO -|- Runner -|- 0x7f988140edc0|| -|- Peak RSS: 25.008 GB