floating point exception raised during step2 SPAtests

saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)

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floating point exception raised during step2 SPAtests #96

Open mstapylton opened 1 year ago

mstapylton commented 1 year ago

We observe this error in v1.1.9

If I replace the binary response variable with a qualitative one step2 runs successfully. Additionally, if I use plink inputs to step2 instead of imputed bgen files it runs successfully. Let me know if I should provide additional information.

without sparse GRM:

with sparse GRM error: Screenshot from 2023-05-24 12-13-21

from core dump: unnamed

Thanks, Matt

saigegit commented 1 year ago

Hi Matt,

Thank you for reporting this issue! The main difference between PLINK and BGEN input is that PLINK contains genotypes with integers while BGEN contains dosages with decimal points. With options --dosage_zerod_cutoff (default=0.2) and --dosage_zerod_MAC_cutoff (default=10). For variants with MAC <= dosage_zerod_MAC_cutoff, dosages <= dosageZerodCutoff with be set to 0. Could you please try to set --dosage_zerod_cutoff=0 to see if the issue with BGEN input persists?

Thanks, Wei