GERMLINE software segfault error

Question

[kiminsigne]

I'm trying to use the GERMLINE software to identify IBD segments. For now, I'm just testing it out on the HapMap Phase II Data (http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2006-07_phaseII/phased/) that they tested it on in their paper. For now I'm just doing chromosome 1 of CEU. However, I'm getting an ambiguous segfault error:

0 SNPs have genetic distance
Read Markers
Reading Markers Complete
Match Markers
Matching Markers - 0%Segmentation fault (core dumped)

At first, after Matching Markers the percentage goes all the way up to 100%, pauses and then the segfault error occurs. Has anyone had a similar problem or can offer a possible explanation? I'm completely lost as to what it could be. Thank you!

Answer 1

[ardi.naseri]

Hi,

I was wondering if you could solve this problem? Actually, I'm trying to run GERMLINE and getting the same error.

Thanks!

[Kip Zimmerman]

The only way I was able to solve this (after trying very many things) was to break up my files by chromosome. This seemed to do the trick. The best guess I have is that it was some sort of memory leak in the c++ program. But I am not entirely sure.

This would not seem to solve the original question above, though.... (since that user was already running on chromosome 1 only)

What kind of format are your files in? PLINK or HapMap? Have you phased them? How are you running your GERMLINE script?