jingydz
commented
1 year ago Error in SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, : LOCO is TRUE but the null model file .rda does not contain LOCO results. In order to apply Leave-one-chromosome-out, please run Step 1 using LOCO. Otherwise, please set LOCO=FALSE in this step (Step 2). Execution halted
I also met a similar problem. Have you solved it?
Hi,
I'm trying to run SAIGE using the example scripts on your website. I have SAIGE version 1.1.5 and Rversion 4.1.3 installed. The error occurs when trying to run step2 after having run step1 of the null model using a full GRM successfully.
The error I receive is:
Error in SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, : unused arguments (idstoExcludeFile = opt$idstoExcludeFile, rangestoExcludeFile = opt$rangestoExcludeFile, sparseSigmaFile = opt$sparseSigmaFile, minInfo = opt$minInfo, IsSingleVarinGroupTest = opt$IsSingleVarinGroupTest, dosageZerodCutoff = opt$dosageZerodCutoff, IsOutputPvalueNAinGroupTestforBinary = opt$IsOutputPvalueNAinGroupTestforBinary, IsAccountforCasecontrolImbalanceinGroupTest = opt$IsAccountforCasecontrolImbalanceinGroupTest, method = opt$method, kernel = opt$kernel, weights.beta.rare = weights.beta.rare, weights.beta.common = weights.beta.common, weightMAFcutoff = opt$weightMAFcutoff, weightsIncludeinGroupFile = opt$weightsIncludeinGroupFile, weights_for_G2_cond = weights_for_G2_cond, IsOutputBETASEinBurdenTest = opt$IsOutputBETASEinBurdenTest, IsOutputHetHomCountsinCaseCtrl = opt$IsOutputHetHomCountsinCaseCtrl, sampleFile_male = opt$sampleFile_male, is_rewrite_XnonPAR_forMales = opt$is_rewrite_XnonPAR_forMales, X_PARregion = opt$X_PARregion, method_to_CollapseUltra Execution halted
Do you have any idea what could be the problem?
Thank you!