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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Segmentation fault (core dumped) #519

Closed ghost closed 7 years ago

ghost commented 7 years ago

Hi there, I try to filter the ExAC database (.vgf.gz) in Linox Bash shell on windows and get a seg fault after about 5 minutes of running fine.

my input: bcftools view -i 'FILTER~"PASS"' ExAC.r0.3.sites.vep.vcf.gz filtered.vcf.gz

last few lines of output:

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

Segmentation fault (core dumped)

thanks a lot for your hints!

pd3 commented 7 years ago

Hi, I was not able to reproduce the error, could you please try with the latest bcftools/htslib version? Please see a description how to obtain it here http://samtools.github.io/bcftools/

My command was

bcftools view -i 'FILTER~"PASS"'  ExAC.r0.3.1.sites.vep.vcf.gz -Ob -o test.bcf
mcshane commented 7 years ago

Closing as cannot reproduce. Please reopen if you can give us more information.