bedtools segmentation fault

Question

[denise.mauldin]

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

[Ashutosh Pandey]

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

[PoGibas]

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