I'm extracting BED from a 77G VCF file using
vcf2bed, and it does a bunch of
core dumps. This is because I'm using the following on a compute node to extract the bed:
PATH=/path/to/bedops/2.4.29/bin/:$PATH switch-BEDOPS-binary-type --megarow cat 77G_vcf.vcf | parallel --pipe vcf2bed --do-not-sort --snvs >snvs.bed
The multiple core dumps happen thanks to the
parallel --pipe, I guess. When I ran this on a login node without the
parallel --pipe and with an
&, I see the process running, but a
jobs shows a core dump happening as well. The BED file grows and looks fine, but the core dump happens nonetheless.
Am I missing something? This worked not 2 days ago.