Question: bedtools segmentation fault
0
gravatar for denise.mauldin
3.6 years ago by
denise.mauldin0 wrote:

Hi all,

 

I have a multi-sample VCF file and the Kaviar VCF file.  I'm doing:

bedtools intersect -sorted -a Family5_sorted.vcf.gz -b Kaviar-150812-ISB-hg19.vcf.gz -wb

It prints 9795 results for chromosome 1 and then dies with a Segementation fault (core dumped).  The line that it dies on doesn't seem to be any different than previous lines.  I've also tried reversing the a and b file and it dies on a different line (but close to where it dies the other way avb is 627982 and bva is 625369).  How do I troubleshoot what's going on?

 

Thanks,

Denise

 

segmentation fault bedtools • 2.2k views
ADD COMMENTlink written 3.6 years ago by denise.mauldin0

Normally this error is associated with low memory (RAM). Try some of the suggested solutions in this post (https://www.biostars.org/p/124620/).

ADD REPLYlink written 3.6 years ago by Ashutosh Pandey11k

Had same problem (as Ashutosh mentioned it was caused by low memory). Either use more powerful machine or try looping through chromosomes.

ADD REPLYlink written 3.6 years ago by PoGibas4.8k
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