GenomicsDBimport multijob issue

I'm having a strange problem with GenomicsDBImport. I'm trying to call SNPs for the full genome, so I've been importing my g.vcfs into a GenomicsDB database per chromosome. Each chromosome is a different job, which I've been launching simultaneously. Each job uses the same set of samples, but is for a different part of the genome. My issue is that when launching the jobs simultaneously, only the first job prints correctly, while the others seem to run but don't give any output. The jobs that don't print correctly, only output a file named "__tiledb_workspace.tdb", which is empty. Despite this, the non-printing jobs seem to continue running and produce a log file saying it worked. If I wait a bit, and launch the jobs separately, they run concurrently fine.

For reference, I'm using GATK 4.beta.3-SNAPSHOT, and I'm launching jobs on a slurm job management system.

Issue · Github
by Sheila

Issue Number
2780
State
closed
Last Updated
Assignee
Array
Closed By
vdauwera

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