We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

GenomicsDBImport creating lots of "temporary" files

Hello, helpful experts of GATK --

I'm running into an issue using GenomicsDBImport on our cluster. It's creating a lot of large "temporary" files on the compute nodes, which remain even after GATK has finished running. The filenames are of this format: "libtiledbgenomicsdb984630309282992004.so". Since I'm working with a transcriptome, I'm running GenomicsDBImport over quite a few different contigs and these files are really adding up. I can manually delete them, but this presents a problem for running batched jobs over multiple days. On one node they took up 90G over a weekend run, which was enough to impact node performance (causing our HPC person to ask me what was going on).

Is there anything I can do about this? I tried GenotypeGVCFs and it was unworkably slow. Wondering if there's a flag I'm missing or something else that will tell GenomicsDBImport to delete these files once it's done with them. I want to be a good cluster user, so it would be great to know if there's an alternative user-side strategy to manually deleting them periodically.

Thank you!
Carolyn

Answers

Sign In or Register to comment.