GenomicsDBImport Batch import with consolidate takes forever

SkyWarriorSkyWarrior TurkeyMember ✭✭✭

Hi. I just came across with this problem. I am using GenomicsDBImport and GenotypeGVCFs from GATK4.0 for trios and small cohorts and I wanted to use the same workflow for my population work as well. However importing over 1000 100X WES samples of hg19 eats a lot of memory so I decided to go with batch import. My batch size is 100 and I import per chromosome. Batch import performance is almost on par with importing without batches however Consolidate step takes forever and never finishes (At least I have not seen it to finish at all. No error messages given. GATK seems to be stuck at that step). One of them has been running for more than 14 hours after batch import at the consolidate step. Am I doing anything wrong or is there a trick about getting consolidate to run faster?

I am running GATK 4.0.3.0 Oracle JDK 1.8.0_161 and Ubuntu 17.10 on kernel 4.15.9 mainline on 128G 10 core system.

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