line 164: 15342 Segmentation fault (core dumped) ${cmd} ${options} - 0<&0

Question

[Niharika]

command I ran:

vcf2bed-megarow < my_sample.vcf.gz --max-mem 127G --sort-tmpdir temp > my_sample.bed

I am using version: 2.4.41 of vcf2bed size of compressed vcf : 48.9 mb

[Pierre Lindenbaum]

what is vcf2bed-megarow ?

[Alex Reynolds]

It is part of BEDOPS.

Answer 1

[Alex Reynolds]

You can't pass a gzipped file to vcf2bed (or vcf2bed-megarow, or any of the convert2bed format translators).

You should extract the gzip file and move the options to the command:

vcf2bed-megarow --max-mem 127G --sort-tmpdir temp < <(gunzip -c my_sample.vcf.gz) > my_sample.bed

Or the equivalent:

gunzip -c my_sample.vcf.gz | vcf2bed-megarow --max-mem 127G --sort-tmpdir temp - > my_sample.bed

You can almost certainly reduce this parameter: --max-mem 127G to something much much lower. It should be less than available system memory, in any case.