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Hi, I am having a similar issue where GenotypeGVCF is taking a long time to finish. Is there a way to get it to use more than a single core? It is also not using all the memory provided to it.
Thank you very much for the suggestions, they seem to have helped and I have finally performed the imports successfully on each chromosome separately. Regarding merging the workspaces, from what ...
I have also encountered the following error on the runs for most of the chromosomes (some finished with no errors) [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit ...
Thanks a lot for the help. I have run the import with each chromosome separately. However I am still unclear on how to merge the resulting genomicsDBs together, and was only able to find https://gi...
Hi, thanks for the reply. I have managed to get it to run by adding a java option to run garbage collection in parallel. Here's the command I'm running right now: gatk GenomicsDBImport --java-optio...