Comments (21)
Hi Nicola,
This error message is usally due to the non-invertible covariate matrix.
Which version of SAIGE are you using? The newer versions > 0.23 would have solved this issue automatically.
Thanks,
Wei
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Interesting. Could you please have a check to see whether the second non-genetic covariate in your formula has identical values for the tested samples?
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Dear Nicola,
Thank you so much for providing more details! Sorry for dropping the ball for a while. I'm happy to help.
You mentioned that when no covariates were used, you saw the same error message.
May I ask how many covariates are used for the jobs shown in the log file?
Thanks,
Wei
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Hi Nicola and Wei,
Hopefully it's already solved, but just in case, other people like me met the same problem. It turns out the variants need to be filtered to at least MAC=1 for any individuals that have phenotype data for the particular trait. It's probably a good idea to include this in QC steps.
Best,
Bin
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Dear Wei, Nicola and Bin,
I hope this problem has been solved. I am sorry that I met a similar issue with my analysis of UK Biobank data. Please kindly see the error in the attached log.
Please kindly note I am using the SAIGE under v 0.29.5. I have also checked my plink file which contains only autosomal variants whose minimum MAF is 1.00e-05.
Any comment or suggestion is appreciated.
Thank you very much!
Best wishes,
Xiao
SAIGE_bi_HPTN_1.log
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@byenj
Hi Bin,
Thank you very much for your reply! However, even I followed your suggestions (MAC=3; only keep samples having both genotype and phenotype data), I still got the same error, but the 'instance' seems changed. Please kindly see the details below.
error: inv_sympd(): matrix is singular or not positive definite
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
compared with last time:
error: inv_sympd(): matrix is singular or not positive definite
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_M_create
Really appreciate you helping me with this!
Many thanks and best wishes,
Xiao
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Hi Xiao,
This issue should have been solved in more recent versions.
Thanks,
Wei
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