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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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SAIGE-GENE+ install #428

Closed jingydz closed 1 year ago

jingydz commented 1 year ago

Command

SAIGE]$ R CMD INSTALL SAIGE

Command

devtools::install_github("weizhouUMICH/SAIGE") Downloading GitHub repo weizhouUMICH/SAIGE@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update? Enter one or more numbers, or an empty line to skip updates: 3 ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/tmp/RtmpRGRf5u/remotes32497f06bb67/weizhouUMICH-SAIGE-a417272/DESCRIPTION’ ... ─ preparing ‘SAIGE’: (1.9s) ✔ checking DESCRIPTION meta-information ─ cleaning src ─ checking whether ‘INDEX’ is up-to-date ... NO ─ use ‘--force’ to remove the existing ‘INDEX’ ─ excluding invalid files (918ms) 。。。 -- Installing: /parastor300/work01/zhangjj/software/SAIGE/thirdParty/cget/cget/pkg/xiaoyeli__superlu/install/include/slu_zdefs.h Successfully installed xiaoyeli/superlu Waf: The wscript in '/parastor300/work01/zhangjj/software/SAIGE/thirdParty/bgen' is unreadable Traceback (most recent call last): File "/parastor300/work01/zhangjj/software/SAIGE/thirdParty/bgen/.waf3-2.0.6-f8aee10f7730da942389d88501d489e8/waflib/Scripting.py", line 101, in waf_entry_point set_main_module(os.path.normpath(os.path.join(Context.run_dir,Context.WSCRIPT_FILE))) File "/parastor300/work01/zhangjj/software/SAIGE/thirdParty/bgen/.waf3-2.0.6-f8aee10f7730da942389d88501d489e8/waflib/Scripting.py", line 141, in set_main_module Context.g_module=Context.load_module(file_path) File "/parastor300/work01/zhangjj/software/SAIGE/thirdParty/bgen/.waf3-2.0.6-f8aee10f7730da942389d88501d489e8/waflib/Context.py", line 360, in load_module exec(compile(code,path,'exec'),module.dict) File "/parastor300/work01/zhangjj/software/SAIGE/thirdParty/bgen/wscript", line 33 print "Creating %s build..." % bld.options.mode ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Creating %s build..." % bld.options.mode)? ERROR: configuration failed for package ‘SAIGE’

  • removing ‘/home2/zhangjj/R/x86_64-conda-linux-gnu-library/4.1/SAIGE’

I have tried two installation methods to install SAIGE-GENE+, but the installation failed. Does anyone know why?

jingydz commented 1 year ago

extdata]$ Rscript step1_fitNULLGLMM.R \

    --plinkFile=./input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly_22chr  \
    --phenoFile=./input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt \
    --phenoCol=y_binary \
    --covarColList=x1,x2,a9,a10 \
    --qCovarColList=a9,a10  \
    --sampleIDColinphenoFile=IID \
    --traitType=binary        \
    --outputPrefix=./output/example_binary \
    --nThreads=24   \
    --IsOverwriteVarianceRatioFile=TRUE

Loading required package: optparse R version 3.6.1 (2019-07-05) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /xxx/anaconda3/envs/RSAIGE/lib/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] optparse_1.6.4 SAIGE_0.45.1

loaded via a namespace (and not attached): [1] compiler_3.6.1 Matrix_1.5-4.1 Rcpp_1.0.1 getopt_1.20.3 [5] grid_3.6.1 RcppParallel_4.4.4 lattice_0.20-38 Error in parse_args(parser, positional_arguments = 0) : Error in getopt(spec = spec, opt = args) : long flag "qCovarColList" is invalid Execution halted

jingydz commented 1 year ago

extdata]$ less cmd.sh extdata]$ Rscript step1_fitNULLGLMM.R \

    --plinkFile=./input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly \
    --phenoFile=./input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt \
    --phenoCol=y_binary \
    --covarColList=x1,x2 \
    --sampleIDColinphenoFile=IID \
    --traitType=binary        \
    --outputPrefix=./output/example_binary_includenonAutoforvarRatio \
    --nThreads=4    \
    --LOCO=FALSE    \
    --minMAFforGRM=0.01

Loading required package: optparse R version 3.6.1 (2019-07-05) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /xxx/anaconda3/envs/RSAIGE/lib/R/lib/libRblas.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] optparse_1.6.4 SAIGE_0.45.1

loaded via a namespace (and not attached): [1] compiler_3.6.1 Matrix_1.5-4.1 Rcpp_1.0.1 getopt_1.20.3 [5] grid_3.6.1 RcppParallel_4.4.4 lattice_0.20-38 $plinkFile [1] "./input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly"

$phenoFile [1] "./input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt"

$phenoCol [1] "y_binary"

$traitType [1] "binary"

$invNormalize [1] FALSE

$covarColList [1] "x1,x2"

$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] "./output/example_binary_includenonAutoforvarRatio"

$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 4 threads are set to be used Error in fitNULLGLMM(plinkFile = opt$plinkFile, phenoFile = opt$phenoFile, : WARNING: The variance ratio file ./output/example_binary_includenonAutoforvarRatio.varianceRatio.txt already exists. The new variance ratios will be output to ./output/example_binary_includenonAutoforvarRatio.varianceRatio.txt. In order to avoid overwriting the file, please remove the ./output/example_binary_includenonAutoforvarRatio.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

jingydz commented 1 year ago

I have successfully installed the software.

$ R

library(SAIGE)