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VT rminfo get's killed #115

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violetbrina opened this issue May 28, 2021 · 0 comments
Open

VT rminfo get's killed #115

violetbrina opened this issue May 28, 2021 · 0 comments

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@violetbrina
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Is there any way to limit the amount of memory vt norm uses? Currently I'm trying to remove the info fields from a massive vcf (>150GB) and the process just dies.

rminfo v0.5

options:     input VCF file                   -
         [o] output VCF file                  reduced/gnomad.genomes.v3.1.1.sites.chr11.vcf
         [q] quiet                            false
         [t] info tags                        popmax,faf95_popmax,AC_non_v2_XX,AN_non_v2_XX and 901 other values

[E::idx_find_and_load] Could not retrieve index file for '-'
Killed

Any way to throttle this? I've tried streaming in the file using bcftools as you can see. If I could set a max mem option then that would be great.

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