Andrius Jonas Dagilis
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Latest activity by Andrius Jonas Dagilis-
Andrius Jonas Dagilis commented,
I will give it a shot! Just about done re-generating gvcfs just in case something went wrong in that process, should have an update for you over the weekend.
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Andrius Jonas Dagilis commented,
Here you go - tried running without the --max-alternate-alleles option and had the same result, so I don't think that option is causing it. Using GATK jar /nas/longleaf/apps/gatk/4.2.4.1/gatk-4.2.4...
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Andrius Jonas Dagilis commented,
Updating to 4.2.4.1 has at least changed the errors, so that's something.I created the databases using the -genomicsdb-shared-poixfs-optimizations parameter, and attempted to run GenotypeGVCFs usin...
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Andrius Jonas Dagilis commented,
Hey Genevieve Brandt (she/her), I let a few different jobs try and run over the weekend and they have all stalled at 200kb in. I have tried: Giving the node more memory overhead (190 for GATK, 260 ...
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Andrius Jonas Dagilis commented,
Thanks Genevieve Brandt (she/her), I've started another job using a different amount of memory, but since it's still in queue, here's the jstack output from one of the jobs: Full thread dump OpenJD...
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Andrius Jonas Dagilis commented,
Hi,Reviving this thread since I've run into a nearly identical issue. I am running GATK 4.1.9.0, and have a data-set of 807 flies for which I am trying to genotype individual chromosomes using the ...