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: "". 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!


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