Error in SAIGE on bioconda

[Amelia-uoft]

Hello,

I am very new to R-SAIGE. I tried to follow https://github.com/weizhouUMICH/SAIGE/issues/272 to install SAIGE package and run your example. I typed "step1_fitNULLGLMM.R --help step2_SPAtests.R --help createSparseGRM.R --help" They all worked. However, I always got the following output when I ran your example. Could you please let me know you suggestions to help solve the problem? Many thanks!

step1_fitNULLGLMM.R \

    --plinkFile=nfam_100_nindep_0_step1_includeMoreRareVariants_poly \

    --phenoFile=pheno_1000samples.txt_withdosages_withBothTraitTypes.txt \

Loading required package: optparse R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Big Sur 10.16

Matrix products: default BLAS/LAPACK: /Users/briolaisnew2/opt/anaconda3/envs/saige/lib/libopenblasp-r0.3.17.dylib

locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] optparse_1.6.6 SAIGE_0.44.5

loaded via a namespace (and not attached): [1] compiler_4.0.5 Matrix_1.3-4 Rcpp_1.0.7 getopt_1.20.3
[5] grid_4.0.5 RcppParallel_5.1.4 lattice_0.20-44
$plinkFile [1] ""

$phenoFile [1] ""

$phenoCol [1] ""

$traitType [1] "binary"

$invNormalize [1] FALSE

$covarColList [1] ""

$sampleIDColinphenoFile [1] "IID"

$tol [1] 0.02

$maxiter [1] 20

$tolPCG [1] 1e-05

$maxiterPCG [1] 500

$nThreads [1] 1

$SPAcutoff [1] 2

$numRandomMarkerforVarianceRatio [1] 30

$skipModelFitting [1] FALSE

$memoryChunk [1] 2

$tauInit [1] "0,0"

$LOCO [1] TRUE

$traceCVcutoff [1] 0.0025

$ratioCVcutoff [1] 0.001

$outputPrefix [1] "~/"

$IsOverwriteVarianceRatioFile [1] FALSE

$IsSparseKin [1] FALSE

$numRandomMarkerforSparseKin [1] 2000

$isCateVarianceRatio [1] FALSE

$relatednessCutoff [1] 0.125

$cateVarRatioMinMACVecExclude [1] "0.5,1.5,2.5,3.5,4.5,5.5,10.5,20.5"

$cateVarRatioMaxMACVecInclude [1] "1.5,2.5,3.5,4.5,5.5,10.5,20.5"

$isCovariateTransform [1] TRUE

$isDiagofKinSetAsOne [1] FALSE

$useSparseSigmaConditionerforPCG [1] FALSE

$useSparseSigmaforInitTau [1] FALSE

$useSparseGRMtoFitNULL [1] FALSE

$minMAFforGRM [1] 0.01

$minCovariateCount [1] -1

$includeNonautoMarkersforVarRatio [1] FALSE

$FemaleOnly [1] FALSE

$MaleOnly [1] FALSE

$sexCol [1] ""

$FemaleCode [1] "1"

$MaleCode [1] "0"

$noEstFixedEff [1] FALSE

$help [1] FALSE

tauInit is 0 0 cateVarRatioMinMACVecExclude is 0.5 1.5 2.5 3.5 4.5 5.5 10.5 20.5 cateVarRatioMaxMACVecInclude is 1.5 2.5 3.5 4.5 5.5 10.5 20.5 Markers in the Plink file with MAF >= 0.01 will be used to construct GRM Error in fitNULLGLMM(plinkFile = opt$plinkFile, phenoFile = opt$phenoFile, : WARNING: The variance ratio file ~/.varianceRatio.txt already exists. The new variance ratios will be output to ~/.varianceRatio.txt. In order to avoid overwriting the file, please remove the ~/.varianceRatio.txt or use the argument outputPrefix_varRatio to specify a different prefix to output the variance ratio(s). Otherwise, specify IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten with new variance ratio(s) Execution halted zsh: command not found: --plinkFile=nfam_100_nindep_0_step1_includeMoreRareVariants_poly zsh: command not found: --phenoFile=pheno_1000samples.txt_withdosages_withBothTraitTypes.txt

[Amelia-uoft]

The example script is working on my computer now.

[jingydz]

I encountered the same problem as you did, and I solved it by adding the command "--IsOverwriteVarianceRatioFile=TRUE".