>|> 20240920 18:04:26.775 -|- INFO -|- AlignSettings -|- 0x7fd7ddc4edc0|| -|- Using 56 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20240920 18:04:26.782 -|- INFO -|- CheckPositionalArgs -|- 0x7fd7ddc4edc0|| -|- READ input file: /pbi/flash/smrtlink/smrtlink-alpha/smrtlink/userdata/jobs_root/0000/0000114/0000114801/cromwell-job/call-isoseq_refine/shard-8/execution/flnc.bam
>|> 20240920 18:04:26.782 -|- INFO -|- CheckPositionalArgs -|- 0x7fd7ddc4edc0|| -|- REF  input file: /pbi/dept/secondary/siv/references/official/Human_hg38_Gencode_v39/human_GRCh38_no_alt_analysis_set.fasta
>|> 20240920 18:04:26.882 -|- WARN -|- operator() -|- 0x7fd7ddc4edc0|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence!
>|> 20240920 18:04:26.883 -|- INFO -|- Index -|- 0x7fd7ddc4edc0|| -|- Start reading/building index
>|> 20240920 18:05:13.496 -|- INFO -|- Index -|- 0x7fd7ddc4edc0|| -|- Finished reading/building index
>|> 20240920 18:06:18.940 -|- INFO -|- operator() -|- 0x7fd7b17d8640|| -|- Merged sorted output from 0 files and 8 in-memory blocks
>|> 20240920 18:06:18.940 -|- INFO -|- Close -|- 0x7fd7ddc4edc0|| -|- Generating BAI
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Mapped Reads: 751899
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Alignments: 757051
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Mapped Bases: 1134614848
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Mean Gap-Compressed Sequence Identity: 99.69%
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Max Mapped Read Length: 7163
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Mean Mapped Read Length: 1498.73
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Index Build/Read Time: 49s 131ms 
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Alignment Time: 1m 819us 
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Sort Merge Time: 1s 957ms 
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- BAI Generation Time: 940ms 603us 
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Run Time: 1m 53s 
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- CPU Time: 1h 662ms 
>|> 20240920 18:06:19.881 -|- INFO -|- Runner -|- 0x7fd7ddc4edc0|| -|- Peak RSS: 20.719 GB