Question: GERMLINE software segfault error
0
gravatar for kiminsigne
4.5 years ago by
kiminsigne0
United States
kiminsigne0 wrote:

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!

 

ibd germline segfault • 1.2k views
ADD COMMENTlink modified 3.3 years ago by ardi.naseri0 • written 4.5 years ago by kiminsigne0
0
gravatar for ardi.naseri
3.3 years ago by
ardi.naseri0 wrote:

Hi,

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

Thanks!

ADD COMMENTlink written 3.3 years ago by ardi.naseri0

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?

ADD REPLYlink written 3.2 years ago by Kip Zimmerman0
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