Question: ShapeIt giving Segfault 11?
1
gravatar for jwhite
2.8 years ago by
jwhite10
United States
jwhite10 wrote:

Hi all,

I'm trying to successfully run SHAPEIT to phase haplotypes but am not having luck. (https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html).

I'm running El Capitan and have downloaded the Mac option from the SHAPEIT webpage. I've recently installed Boost libraries using

brew install boost

Then, I navigated both the SHAPEIT exe file and the following example files into a new folder called "Test". So the Test folder has: genetic_map.txt, gwas.bed, gwas.bim, gwas.fam, and shapeit

The code I'm trying to run is from the "Getting Started" tab of the SHAPEIT website

./shapeit --input-bed gwas.bed gwas.bim gwas.fam \
          --input-map genetic_map.txt \
          --output-max gwas.phased.haps gwas.phased.sample ;

The problem is that I get the message:

Segmentation fault: 11

I've Googled, and as best I can figure out is that this problem results when a program tries to call memory that it's not allowed to call and usually you can fix it by going into the code directly to change settings. It seems like it's an error that developers usually run into. Since I don't have the code for SHAPEIT and I'm a coding novice, I'm at a loss for what to do next. I've tried the same piece of code on another Mac running Mavericks and the same error resulted.

Has anyone else run into this issue? Does anyone have suggestions?

Thanks!

software error • 1.5k views
ADD COMMENTlink modified 2.8 years ago by cae8030 • written 2.8 years ago by jwhite10

The latest Mac download at the site you linked is for v. 10.9.x. You are assuming that it will actually work on the latest Mac OS. I suggest that you email the authors and ask about compatibility.

ADD REPLYlink written 2.8 years ago by genomax65k

I thought compatibility might be the issue as well, so I tried the same piece of code on another (bigger) Mac that is running 10.9 and got the same error.

ADD REPLYlink written 2.8 years ago by jwhite10
0
gravatar for cae803
2.8 years ago by
cae8030
Japan
cae8030 wrote:

I had the same trouble. So I am using the earlier version of SHAPEIT.v2.r790 here. I referred a post of the OXSTATGEN mailing list.

ADD COMMENTlink written 2.8 years ago by cae8030
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