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?