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What would cause Mutect2 to run super slow?
I'm running Mutect2 from GATK 220.127.116.11 on a cohort of TCGA T/N pairs. About half of them finished in 8-16 hours, but the other half have been running extremely slowly. They are verging on about 4 solid days of compute, and seem to be only on chromosome 3.
I'm running with the --germline-resource af-only-gnomad.hg38.vcf.gz downloaded from the Broad, and a set of merged intervals of hg38 exons (306k regions total). and using the GDC GRCh38 reference fasta.
As far as I can tell, the compute nodes are running find and not overloaded. Mutect has plenty of RAM
Here's a section of the stdout/stderr, which seems to not list any errors, just some warning about lack of AVX instructions preciptating a "MUCH slower LOGLESS_CACHING implementation!"
18:26:42.675 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
18:27:04.057 INFO ProgressMeter - chr1:184914 0.4 120 336.8
18:27:16.799 INFO ProgressMeter - chr1:841791 0.6 410 720.9
18:27:28.881 INFO ProgressMeter - chr1:941067 0.8 560 727.2
18:27:48.734 INFO ProgressMeter - chr1:944364 1.1 580 526.8
18:28:00.608 INFO ProgressMeter - chr1:957920 1.3 620 477.3
15:36:21.119 INFO ProgressMeter - chr3:138324466 5589.6 224460 40.2
15:36:35.178 INFO ProgressMeter - chr3:138398460 5589.9 224490 40.2
15:36:47.696 INFO ProgressMeter - chr3:138467552 5590.1 224540 40.2
After the first 5 minutes of processing, the "Regions/Minute" has dropped below 200, and has mostly hovered in the ~40 range, with a minimum of 39.3.
Any ideas? How much -Xmx should I be giving Mutect2 with a standard human genome?