Dear developers I am currently running a ukbb analysis using version 1.1.3 (for step 2) step1 ran on version 1.1.
When running
SPAGMMATtest(bgenFile="bulk-data/22828/v3/ukb_imp_chr7_v3.bgen", bgenFileIndex="bulk-data/22828/v3/ukb_imp_chr7_v3.bgen.bgi",sampleFile="samplefile.txt",GMMATmodelFile="/SAIGE/BMD_prefered.rda", varianceRatioFile="SAIGE/BMD_prefered.varianceRatio.txt", is_imputed_data=TRUE,SAIGEOutputFile="./BMD_eu_chr7.txt", chrom=7)
I received the error
No markers on chrom 7 are found
So after some days today I just tried to run the same command with the option LOCO=FALSE, as I do not see how this in previous SAIGE versions use to work properly and now it does not...
This time it runs but I get the following error
Error in mainMarkerInCPP(genoType, traitType, genoIndex_prev, genoIndex, :
Error in function boost::math::quantile(const normal_distribution&, double): Probability argument is nan, but must be >= 0 and <= 1 !
These are files directly downloaded from the UKBB application, so I really do not follow what is wrong. Is there a problem of SAIGE reading the files?
Dear developers I am currently running a ukbb analysis using version 1.1.3 (for step 2) step1 ran on version 1.1. When running SPAGMMATtest(bgenFile="bulk-data/22828/v3/ukb_imp_chr7_v3.bgen", bgenFileIndex="bulk-data/22828/v3/ukb_imp_chr7_v3.bgen.bgi",sampleFile="samplefile.txt",GMMATmodelFile="/SAIGE/BMD_prefered.rda", varianceRatioFile="SAIGE/BMD_prefered.varianceRatio.txt", is_imputed_data=TRUE,SAIGEOutputFile="./BMD_eu_chr7.txt", chrom=7) I received the error No markers on chrom 7 are found
So after some days today I just tried to run the same command with the option LOCO=FALSE, as I do not see how this in previous SAIGE versions use to work properly and now it does not... This time it runs but I get the following error
Error in mainMarkerInCPP(genoType, traitType, genoIndex_prev, genoIndex, : Error in function boost::math::quantile(const normal_distribution&, double): Probability argument is nan, but must be >= 0 and <= 1 !
These are files directly downloaded from the UKBB application, so I really do not follow what is wrong. Is there a problem of SAIGE reading the files?