Open medinacarolina opened 1 year ago
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="/home/r549001/ukb/SAIGE/BMD_prefered.rda", varianceRatioFile="/home/r549001/ukb/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
I have ran this before, in version 0.44 for another phenotype and found no error. Could you guide me in what could be going on? Carolina
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="/home/r549001/ukb/SAIGE/BMD_prefered.rda", varianceRatioFile="/home/r549001/ukb/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
I have ran this before, in version 0.44 for another phenotype and found no error. Could you guide me in what could be going on? Carolina