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weizhouUMICH / SAIGE

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SAIGE running error #344

Closed huanghe0220 closed 2 years ago

huanghe0220 commented 3 years ago

Hi @weizhou0 @weizhouUMICH @matuskosut and others: I downloaded the saige with conda following this instructionhttps://github.com/weizhouUMICH/SAIGE/issues/272 conda create -n saige -c conda-forge -c bioconda r-base=3.6.1 r-saige=0.38.8.8 savvy=1.3.0 r-optparse=1.6.2=r36h6115d3f_1 And succeeded in these three steps step1_fitNULLGLMM.R --help step2_SPAtests.R --help createSparseGRM.R --help

However, when I ran step 1(Rscript step1_fitNULLGLMM.R) with my own dataset, I got a bug like this: Error in terms.formula(formula, data = data) : invalid model formula in ExtractVars

when I ran step 1 with the example dataset, I got Error in fitNULLGLMM(plinkFile = opt$plinkFile, phenoFile = opt$phenoFile, : unused arguments (IsOverwriteVarianceRatioFile = opt$IsOverwriteVarianceRatioFile, includeNonautoMarkersforVarRatio = opt$includeNonautoMarkersforVarRatio, sexCol = opt$sexCol, FemaleCode = opt$FemaleCode, FemaleOnly = opt$FemaleOnly, MaleCode = opt$MaleCode, MaleOnly = opt$MaleOnly, noEstFixedEff = opt$noEstFixedEff, useSparseGRMtoFitNULL = opt$useSparseGRMtoFitNULL)

If I annotate those argument then ran step 2(Rscript step2_SPAtests.R) with the example dataset, I bumped into Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : long flag "dosageFile" is invalid

I don't know why this happened. Do you have any advise? Looking forward to your reply.

Best, Huang He

matuskosut commented 3 years ago

Hi @huanghe0220 , can you try to recreate environment in simple way

conda create -n saige -c conda-forge -c bioconda -y r-base=3.6.3 r-saige=0.35.8.8
conda activate saige

What is the output of this command?

which step2_SPAtests.R

When you run help do you get correct version of saige in the output?

step2_SPAtests.R --help

ps: step1 says unused arguments, good to read older issues or wiki

weizhouUMICH commented 2 years ago

Sorry fo the late reply! We have just released a new version 1.0.0. It has substantial computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests and clearer log output. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ The program will be maintained by multiple SAIGE developers there. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei