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3.8 years ago
MAPK
★
2.1k
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
