empty output for binary trait

[iamhere218]

Hello, I tried SAIGE 0.44.1, 0.44.2 as well as 0.39.2 on my dataset and had empty output at step1 for my binary trait analysis. Could you please help to clarify the issue why? Thank you!

[sunghe@cn0941 SAIGE]$ step1_fitNULLGLMM.R --plinkFile=AMBiGen_frz3_wes_qc10_autosome_call100 --phenoFile=/data/sunghe/AMBiGen/pheno/4_combine/AMBiGen_frz3_wes_anal_1162.phe --phenoCol=Narrow_01 --sampleIDColinphenoFile=IID --traitType=Binary --LOCO=FALSE --outputPrefix=AMBiGen_frz3_wes_qc10_autosome_call100_step1 --nThreads=4 --IsOverwriteVarianceRatioFile=TRUE
Loading required package: optparse R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS

Matrix products: default BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] optparse_1.6.6 SAIGE_0.44.2

loaded via a namespace (and not attached): [1] compiler_3.5.1 Matrix_1.2-14 Rcpp_1.0.6 getopt_1.20.3
[5] grid_3.5.1 RcppParallel_5.0.3 lattice_0.20-35
$plinkFile [1] "AMBiGen_frz3_wes_qc10_autosome_call100"

$phenoFile [1] "/data/sunghe/AMBiGen/pheno/4_combine/AMBiGen_frz3_wes_anal_1162.phe"

$phenoCol [1] "Narrow_01"

$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] 4

$SPAcutoff [1] 2

$numRandomMarkerforVarianceRatio [1] 30

$skipModelFitting [1] FALSE

$memoryChunk [1] 2

$tauInit [1] "0,0"

$LOCO [1] FALSE

$traceCVcutoff [1] 0.0025

$ratioCVcutoff [1] 0.001

$outputPrefix [1] "AMBiGen_frz3_wes_qc10_autosome_call100_step1"

$IsOverwriteVarianceRatioFile [1] TRUE

$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 4 threads are set to be used
The variance ratio file AMBiGen_frz3_wes_qc10_autosome_call100_step1.varianceRatio.txt already exists. IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten 1162 samples have genotypes formula is Narrow_01~ 1 980 samples have non-missing phenotypes 182 samples in geno file do not have phenotypes 980 samples will be used for analysis [sunghe@cn0941 SAIGE]$ [sunghe@cn0941 SAIGE]$ ll AMBiGen_frz3_wes_qc10_autosome_call100_step1.* -rw-r----- 1 sunghe sunghe 2788 Apr 8 10:16 AMBiGen_frz3_wes_qc10_autosome_call100_step1.log -rw-r----- 1 sunghe sunghe 0 Apr 8 10:11 AMBiGen_frz3_wes_qc10_autosome_call100_step1.rda -rw-r----- 1 sunghe sunghe 0 Apr 8 10:11 AMBiGen_frz3_wes_qc10_autosome_call100_step1.varianceRatio.txt

[weizhouUMICH]

Hi @iamhere218,

It seems the program stopped at the "980 samples will be used for analysis" and never continue. Can you try to set --traitType="binary" instead of "Binary"?

Thanks, Wei

[iamhere218]

Thank you for your reply. Yes, it worked with "binary" instead of "Binary"........ Thank you!