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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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Performance expectation on highly polygenic GWAS for GCTA-COJO #110

Open vforget opened 5 days ago

vforget commented 5 days ago

Hi,

What is the general performance expectation for highly polygenic GWAS, with hundreds of GWAS-sig loci?

I am running GCTA-COJO conditional analysis on a case:control GWAS with hundreds of loci. Each chromosome runs independently on separate hardware and each node has 16 cores and 128 GB memory. The smaller chromosomes take ~24 hours to complete. I have yet to see a larger chromosome complete. Should I expect this to complete, and there is a underlying issue, or should I just wait.

Thanks,

Vince

anglixue commented 3 days ago

Hi Vince,

It is unusual to run COJO for ~24hours.

Could you provide your command and log file? What files did you input after flag --bfile?

Angli