Floating point exception(core dumped) about saige HOT 6 CLOSED

Did you see the error when LOCO=FALSE?

from saige.

Yes, I receive the same error.

from saige.

Hi @FinSalMar,
Could you please try the newest version to see if the error persists? I'm so sorry for taking so long to get back to you. Please reopen this issue if the error is still seen.

Thanks,
Wei

from saige.

Hi Wei,

I also got the same error in step 1: Floating point exception (core dumped).

The problem comes from a division by 0 in file: src/SAIGE_fitGLMM_fast.cpp
when all individuals in the subset have missing data for a given variant.

The line with the error is:
freq = sum(m_OneSNP_Geno)/float((2*(Nnomissing-lengthIndexNA)));

It fails when Nnomissing == lengthIndexNA.

This happend to me when running a GWAS on females, where the genotype file included Y chromosome.
A quick work around was to remove chrY from the genotype file.

But it would be nice if the program could automatically skip variants where:
Nnomissing == lengthIndexNA

Thanks

from saige.

Hi Laurent,

Thanks for reporting this! This issue should has been fixed since the version 0.36.4.
#154

Could you please try the newest version 0.36.5?
https://github.com/weizhouUMICH/SAIGE#log-for-fixing-bugs

Thanks
Wei

from saige.

Yes it is working with version 0.36.5.
Thanks

from saige.