'std::bad_alloc'

[Abdoulis21]

Hello Joseph!

Thank you so much for your great program! The original publication of fGWAS is a very nice read too.

I am having problems running fGWAS though. I get the following error message:

terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

Do you know what might be causing it? I must warn you that the input file contains ~30M SNPs. When I load a single chromosome only, fGWAS seems to run. I tried increasing -k but didn't seem to solve the problem.

Any help/insight would be much appreciate it!

Best,
Abdou

[Jeremy37]

This just sounds like you are running out of memory. Are you running on a cluster, and if so, can you increase the memory allocation you request?
If you can't access more memory, then how many annotations are in your file? Are you using them all, or could you trim the file first?
Lastly, do you need all 30M SNPs, or could you trim out regions of the genome that aren't of interest? This could also improve your run time.

[Abdoulis21]

Dear Joseph,

Thank you very much for your answer.

It was indeed a memory error. I was able after all to load all the SNPs. I am sorry to have bothered you with such a thing.

Thank you again for fGWAS, it's a great piece of work!

Best,
Abdou