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Parallel submission of GATK GenomicsDBImport

I have been trying to submit GATK jobs for chr1 to chrY as below; but not sure why it's not working. It works individually, but when I use parallel the process doesn't do anything after creating the .tdb and json files. Just wondering if I am missing something. Can someone please help me figure out the problem. Thanks for you help in advance!

parallel '/usr/local/gatk-4.1.7.0/gatk --java-options "-Xms4G -Xmx32G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
 GenomicsDBImport \
--genomicsdb-workspace-path /SNPs/TEST/chr{} \
--batch-size 50 \
-L /SNPs/TEST/chr{}.output.bed \
--sample-name-map /home/mylist{}.list \
--tmp-dir=/data/tmp \
--reader-threads 10 \
--max-num-intervals-to-import-in-parallel 10' ::: {1..22} X Y
gatk
• 374 views • link
written by MAPK MAPK

<sing> Not workiiing is not a proper eeeeror meeeeesaaaaaaaage </sing>

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written by ATpoint ATpoint

Not working as in unable to generate even an error message that can be posted. Likely the command syntax is the issue. Not a parallel user myself so can't help.

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written by GenoMax GenoMax

That's exactly what I meant. Sorry that I was not clear with my words. Actually, the process doesn't do anything after creating the .tdb and json files when I use parallel method.

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written by MAPK MAPK

Try to run the code outside of parallel on a small subset for a single chromosome to debug the process. If that works go back to parallel.

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written by ATpoint ATpoint

It works without parallel.

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written by MAPK MAPK

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