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3. GATK4 - Parallelizing genotypegvcfs

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.  

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• Ivan
• December 09, 2020 10:11
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3. GenomicsDBImport running out of memory?

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 ...

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• Ivan
• November 03, 2020 11:51
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3. GenomicsDBImport running out of memory?

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 ...

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• Ivan
• November 02, 2020 09:59
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3. GenomicsDBImport running out of memory?

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...

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• Ivan
• November 02, 2020 09:51
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3. GenomicsDBImport running out of memory?

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...

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• Ivan
• October 28, 2020 19:48
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