Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.