Error in step 2 with quantative trait

[claudiamoreau]

Hi,
I get this error in step 2 when I run step 1 fitting the model with a quantitative trait using a sparse matrix:
Error in function boost::math::quantile(const normal_distribution&, double): Probability argument is -nan, but must be >= 0 and <= 1

When I run the same step 2 with a binary trait in step 1 this does not happen.

Here is my code:
Rscript /lustre03/project/6033529/DM1/scripts/corrected_step1_fitNULLGLMM.r
--bedFile ${ht_data_dir}/${ht_file}.bed
--bimFile ${ht_data_dir}/${ht_file}.bim
--famFile ${ht_data_dir}/${ht_file}.fam
--phenoFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/dorsi_clean.csv
--isCateVarianceRatio=FALSE
--phenoCol=${pheno}
--covarColList=sex
--sampleIDColinphenoFile=IID
--traitType=quantitative
--invNormalize=TRUE
--outputPrefix=/lustre03/project/6033529/DM1/results/genotypes/gwas/${ht_file}sparse${pheno}
--outputPrefix_varRatio=/lustre03/project/6033529/DM1/results/genotypes/gwas/${ht_file}sparse${pheno}_var
--useSparseGRMtoFitNULL=TRUE
--sparseGRMFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/dm1_cag_sag_cluster_noAT-GC_relatednessCutoff_0_2000_randomMarkersUsed.sparseGRM.mtx
--sparseGRMSampleIDFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/dm1_cag_sag_cluster_noAT-GC_relatednessCutoff_0_2000_randomMarkersUsed.sparseGRM.mtx.sampleIDs.txt
--LOCO=FALSE
--IsOverwriteVarianceRatioFile=TRUE

Rscript /lustre03/project/6033529/DM1/scripts/corrected_step2_SPAtests.r
--bedFile ${ht_data_dir}/${ht_file}.bed
--bimFile ${ht_data_dir}/${ht_file}.bim
--famFile ${ht_data_dir}/${ht_file}.fam
--chrom=${ch}
--SAIGEOutputFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/${ht_file}sparse${pheno}_${inds}_chr${ch}_SPA
--minMAF=0
--minMAC=0.5
--LOCO=FALSE
--sparseGRMFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/dm1_cag_sag_cluster_noAT-GC_relatednessCutoff_0_2000_randomMarkersUsed.sparseGRM.mtx
--sparseGRMSampleIDFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/dm1_cag_sag_cluster_noAT-GC_relatednessCutoff_0_2000_randomMarkersUsed.sparseGRM.mtx.sampleIDs.txt
--GMMATmodelFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/${ht_file}sparse${pheno}.rda
--varianceRatioFile=/lustre03/project/6033529/DM1/results/genotypes/gwas/${ht_file}sparse${pheno}_var.varianceRatio.txt

Thanks!