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weizhou0 / qtl

GNU General Public License v3.0
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Error in .Call("_SAIGE_setgenoNULL", PACKAGE = "SAIGE") #1

Closed Antidington closed 10 months ago

Antidington commented 10 months ago

Hi Dr. Zhou,

I pulled the image from Docker Hub, but when I ran the example file provided on your official website, an error occurred, displaying the following message:

root@236451f5d5eb:/app# Rscript step1_fitNULLGLMM_qtl.R \
>         --useSparseGRMtoFitNULL=FALSE  \
>         --useGRMtoFitNULL=FALSE \
>         --phenoFile=./input/seed_1_100_nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_Poisson.txt \
>         --phenoCol=gene_1       \
>         --covarColList=X1,X2,pf1,pf2    \
>         --sampleCovarColList=X1,X2      \
>         --sampleIDColinphenoFile=IND_ID \
>         --traitType=count \
>         --outputPrefix=./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1 \
>         --skipVarianceRatioEstimation=FALSE  \
>         --isRemoveZerosinPheno=FALSE \
>         --isCovariateOffset=FALSE  \
>         --isCovariateTransform=TRUE  \
>         --skipModelFitting=FALSE  \
>         --tol=0.00001   \
>         --plinkFile=./input/n.indep_100_n.cell_1_01.step1       \
>         --IsOverwriteVarianceRatioFile=TRUE
Loading required package: optparse
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

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_1.7.3 SAIGEQTL_0.1.0

loaded via a namespace (and not attached):
[1] compiler_3.6.3      Matrix_1.6-3        Rcpp_1.0.7
[4] getopt_1.20.4       RcppNumerical_0.6-0 grid_3.6.3
[7] data.table_1.12.8   RcppParallel_5.1.7  lattice_0.20-40
$plinkFile
[1] "./input/n.indep_100_n.cell_1_01.step1"

$bedFile
[1] ""

$bimFile
[1] ""

$famFile
[1] ""

$phenoFile
[1] "./input/seed_1_100_nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_Poisson.txt"

$phenoCol
[1] "gene_1"

$isRemoveZerosinPheno
[1] FALSE

$traitType
[1] "count"

$invNormalize
[1] FALSE

$covarColList
[1] "X1,X2,pf1,pf2"

$sampleCovarColList
[1] "X1,X2"

$longlCol
[1] ""

$qCovarColList
[1] ""

$sampleIDColinphenoFile
[1] "IND_ID"

$tol
[1] 1e-05

$maxiter
[1] 20

$tolPCG
[1] 1e-05

$maxiterPCG
[1] 500

$nThreads
[1] 1

$SPAcutoff
[1] 2

$numRandomMarkerforVarianceRatio
[1] 30

$skipModelFitting
[1] FALSE

$skipVarianceRatioEstimation
[1] FALSE

$memoryChunk
[1] 2

$tauInit
[1] "0,0"

$LOCO
[1] TRUE

$isLowMemLOCO
[1] FALSE

$traceCVcutoff
[1] 0.0025

$nrun
[1] 30

$ratioCVcutoff
[1] 0.001

$outputPrefix
[1] "./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1"

$outputPrefix_varRatio
[1] ""

$IsOverwriteVarianceRatioFile
[1] TRUE

$sparseGRMFile
[1] ""

$sparseGRMSampleIDFile
[1] ""

$isCateVarianceRatio
[1] FALSE

$relatednessCutoff
[1] 0

$cateVarRatioMinMACVecExclude
[1] "10,20.5"

$cateVarRatioMaxMACVecInclude
[1] "20.5"

$isCovariateTransform
[1] TRUE

$isDiagofKinSetAsOne
[1] FALSE

$useSparseGRMtoFitNULL
[1] FALSE

$useSparseGRMforVarRatio
[1] FALSE

$minMAFforGRM
[1] 0.01

$maxMissingRateforGRM
[1] 0.15

$minCovariateCount
[1] -1

$includeNonautoMarkersforVarRatio
[1] FALSE

$FemaleOnly
[1] FALSE

$MaleOnly
[1] FALSE

$sexCol
[1] ""

$FemaleCode
[1] "1"

$MaleCode
[1] "0"

$isCovariateOffset
[1] FALSE

$SampleIDIncludeFile
[1] ""

$VmatFilelist
[1] ""

$VmatSampleFilelist
[1] ""

$useGRMtoFitNULL
[1] FALSE

$help
[1] FALSE

tauInit  is  0 0
cateVarRatioMinMACVecExclude  is  10 20.5
cateVarRatioMaxMACVecInclude  is  20.5
Error in .Call("_SAIGE_setgenoNULL", PACKAGE = "SAIGE") :
  "_SAIGE_setgenoNULL" not available for .Call() for package "SAIGE"
Calls: fitNULLGLMM_multiV -> setgenoNULL

How can I solve this problem? Thanks!

weizhou0 commented 10 months ago

Hi @Antidington,

Thank you for reporting the error! It is because we changed the R package name from SAIGE to SAIGEQTL for the github release but the names of pre-compiled files were not updated. Now the github and docker has been updated. Please feel free to give it a try.

Thanks, Wei

Antidington commented 10 months ago

Hi @Antidington,

Thank you for reporting the error! It is because we changed the R package name from SAIGE to SAIGEQTL for the github release but the names of pre-compiled files were not updated. Now the github and docker has been updated. Please feel free to give it a try.

Thanks, Wei

Hi Wei,

It works for me!

Many Thanks, Jichen