>|> 20251018 02:43:29.839 -|- INFO -|- AlignSettings -|- 0x14e72d14c200|| -|- Using 48 threads for alignments, 8 threads for sorting, and 6G bytes RAM for sorting.
>|> 20251018 02:43:29.839 -|- INFO -|- CheckPositionalArgs -|- 0x14e72d14c200|| -|- READ input file: "/mmfs1/gscratch/scrubbed/sr320/github/project-lake-trout/data/pacbio-reads/m84082_250614_081210_s3.hifi_reads.bam"
>|> 20251018 02:43:29.839 -|- INFO -|- CheckPositionalArgs -|- 0x14e72d14c200|| -|- REF  input file: "/mmfs1/gscratch/scrubbed/sr320/github/project-lake-trout/data/GCF_016432855.1_SaNama_1.0_genomic.fna.gz"
>|> 20251018 02:43:29.867 -|- INFO -|- Index -|- 0x14e72d14c200|| -|- Start reading/building index
>|> 20251018 02:43:53.306 -|- INFO -|- Index -|- 0x14e72d14c200|| -|- Finished reading/building index
>|> 20251018 05:48:29.430 -|- INFO -|- operator() -|- 0x14e726eba6c0|| -|- Merged sorted output from 176 files and 8 in-memory blocks
>|> 20251018 05:48:29.431 -|- INFO -|- Close -|- 0x14e72d14c200|| -|- Generating BAI
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Mapped Reads: 8880212
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Alignments: 11666851
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Mapped Bases: 57554511586
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Mean Gap-Compressed Sequence Identity: 98.2721%
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Max Mapped Read Length: 51651
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Mean Mapped Read Length: 4933.17
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Index Build/Read Time: 24s 839ms 
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Alignment Time: 2h 51m 
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Sort Merge Time: 13m 5s 
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- BAI Generation Time: 1m 31s 
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Run Time: 3h 6m 
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- CPU Time: 3d 4h 
>|> 20251018 05:50:00.841 -|- INFO -|- Runner -|- 0x14e72d14c200|| -|- Peak RSS: 48.649 GB