Question: Segmentation fault error while running extractPIRs from ShapeIT
0
gravatar for kirannbishwa01
3.5 years ago by
kirannbishwa011.2k
United States
kirannbishwa011.2k wrote:

I am getting 'segmentation fault error' while trying to run subcommand from ShapeIt

$extractPIRs --bam bamlist --vcf sequence.multiple.vcf.gz --out myPIRsList Reading genotypes in [sequence.multiple.vcf.gz] in VCF format Segmentation fault (core dumped)

This is just a test run using the example file that came with the program. Can't seem to find the cause of it.

Thanks much,

ADD COMMENTlink written 3.5 years ago by kirannbishwa011.2k

Hello! Did you find the reason behind the segmentation fault error? Mine comes without the core dumped statement. It looks like this: /var/spool/pbs/mom_priv/jobs/8948248.wlm01.SC: line 35: 3365 Segmentation fault

Sincerely, Amit

ADD REPLYlink written 5 months ago by amitgourav.ghosh1260
1

That was 3 years ago. Sorry to say, that I dont remember the context of the problem right now.

Not sure, but If you are trying to extract readbackedphased haplotype and runs phasing VCF-SIMPLIFY https://github.com/everestial/VCF-Simplify and other tools in my repo could be helpful.

Thanks,

ADD REPLYlink written 5 months ago by kirannbishwa011.2k

No worries!

Thank you very much for your help.

Sincerely, Amit

ADD REPLYlink written 5 months ago by amitgourav.ghosh1260
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