I have managed to get the step1 run in the server, however I face consistent yet non-understandable issue
I am running 4 GWASes: 2 traits * 2 chips.
The two traits are called YAOSP and YOBP, and somehow YAOSP does not run but the generation of the output halts near the end whereas YOBP run and generates the output fully. For YAOSP, the trait generates more than 200 threads although I have notified that the nThreads to be 15. The output that does not progresses for YAOSP, while the completed output for YOBP are attached. As you can see the variance ratio is not calculated but seem to face bug. Ihave run step1 of all 4 GWASes but YOBP was completed within a few hours whereas YAOSP was like that for days and uses all the threads in the server (which made me to be contacted by the IT department for using all the threads)
The following are my codes for 4 GWASes
step1_fitNULLGLMM.R \
--plinkFile=$genPath/SWE_GSA/SWE_GSA_pi_case_noOverlapOE_QC_auto \
--phenoFile=$phenoCovarPath/phenoCovar_YAOSP_GSA_GWSS_240511.txt \
--phenoCol=Status \
--covarColList=YOB_std,AAO_std,PC1,PC2,PC3,PC4 \
--eventTimeCol=YAOSP \
--sampleIDColinphenoFile=MMSID \
--traitType=survival \
--outputPrefix=$outPath/YAOSP_GSA_240511 \
--nThreads=20 \
--maxiter 5000 \
--LOCO=TRUE \
--minMAFforGRM=0.01 \
--skipModelFitting=FALSE \
--tauInit=1,0 \
--pcgforUhatforSurvAnalysis=FALSE \
--numRandomMarkerforVarianceRatio=1000
I have managed to get the step1 run in the server, however I face consistent yet non-understandable issue I am running 4 GWASes: 2 traits * 2 chips. The two traits are called YAOSP and YOBP, and somehow YAOSP does not run but the generation of the output halts near the end whereas YOBP run and generates the output fully. For YAOSP, the trait generates more than 200 threads although I have notified that the nThreads to be 15. The output that does not progresses for YAOSP, while the completed output for YOBP are attached. As you can see the variance ratio is not calculated but seem to face bug. Ihave run step1 of all 4 GWASes but YOBP was completed within a few hours whereas YAOSP was like that for days and uses all the threads in the server (which made me to be contacted by the IT department for using all the threads)
The following are my codes for 4 GWASes step1_fitNULLGLMM.R \ --plinkFile=$genPath/SWE_GSA/SWE_GSA_pi_case_noOverlapOE_QC_auto \ --phenoFile=$phenoCovarPath/phenoCovar_YAOSP_GSA_GWSS_240511.txt \ --phenoCol=Status \ --covarColList=YOB_std,AAO_std,PC1,PC2,PC3,PC4 \ --eventTimeCol=YAOSP \ --sampleIDColinphenoFile=MMSID \ --traitType=survival \ --outputPrefix=$outPath/YAOSP_GSA_240511 \ --nThreads=20 \ --maxiter 5000 \ --LOCO=TRUE \ --minMAFforGRM=0.01 \ --skipModelFitting=FALSE \ --tauInit=1,0 \ --pcgforUhatforSurvAnalysis=FALSE \ --numRandomMarkerforVarianceRatio=1000
Rscript step2_SPAtests.R \ --vcfFile=$genPath/SWE_GSA/SWE_GSA_pi_case_noOverlapOE_QC_auto.vcf.gz \ --vcfFileIndex=$genPath/SWE_GSA/SWE_GSA_pi_case_noOverlapOE_QC_auto.vcf.gz.csi \ --vcfField=GT \ --chrom=1-22 \ --minMAF=0.001 \ --minMAC=1 \ --sampleFile=$phenoCovarPath/MMSID_phenoCovar_YAOSP_GSA_GWSS_240511.txt \ --GMMATmodelFile=$outPath/YAOSP_GSA_240511.rda \ --varianceRatioFile=$outPath/YAOSP_GSA_240511.varianceRatio.txt \ --SAIGEOutputFile=$outPath/tte_YAOSP_GSA_240511.txt \ --numLinesOutput=2 \ --IsOutputAFinCaseCtrl=TRUE \ --IsOutputNinCaseCtrl=TRUE \ --IsSPAfast=TRUE
YOBP_GSA
step1_fitNULLGLMM.R \ --plinkFile=$genPath/SWE_GSA/SWE_GSA_pi_case_noOverlapOE_QC_auto \ --phenoFile=$phenoCovarPath/phenoCovar_YOBP_GSA_GWSS_240511.txt \ --phenoCol=Status \ --covarColList=YOB_std,SEX,PC1,PC2,PC3,PC4 \ --eventTimeCol=YOBP \ --sampleIDColinphenoFile=MMSID \ --traitType=survival \ --outputPrefix=$outPath/YOBP_GSA_240511 \ --nThreads=18 \ --maxiter 5000 \ --LOCO=TRUE \ --minMAFforGRM=0.01 \ --skipModelFitting=FALSE \ --tauInit=1,0 \ --pcgforUhatforSurvAnalysis=FALSE \ --numRandomMarkerforVarianceRatio=1000
SWE_OE
YAOSP_OE
step1_fitNULLGLMM.R \ --plinkFile=$genPath/SWE_OE/SWE_OE_pi_case_QC_auto \ --phenoFile=$phenoCovarPath/phenoCovar_YAOSP_OE_GWSS_240511.txt \ --phenoCol=Status \ --covarColList=YOB_std,AAO_std,PC1,PC2,PC3,PC4 \ --eventTimeCol=YAOSP \ --sampleIDColinphenoFile=MMSID \ --traitType=survival \ --outputPrefix=$outPath/YAOSP_OE_240511 \ --nThreads=20 \ --maxiter 5000 \ --LOCO=TRUE \ --minMAFforGRM=0.01 \ --skipModelFitting=FALSE \ --tauInit=1,0 \ --pcgforUhatforSurvAnalysis=FALSE \ --numRandomMarkerforVarianceRatio=1000
YOBP_OE
step1_fitNULLGLMM.R \ --plinkFile=$genPath/SWE_OE/SWE_OE_pi_case_QC_auto \ --phenoFile=$phenoCovarPath/phenoCovar_YOBP_OE_GWSS_240511.txt \ --phenoCol=Status \ --covarColList=YOB_std,SEX,PC1,PC2,PC3,PC4 \ --eventTimeCol=YOBP \ --sampleIDColinphenoFile=MMSID \ --traitType=survival \ --outputPrefix=$outPath/YOBP_OE_240511 \ --nThreads=18 \ --maxiter 5000 \ --LOCO=TRUE \ --minMAFforGRM=0.01 \ --skipModelFitting=FALSE \ --tauInit=1,0 \ --pcgforUhatforSurvAnalysis=FALSE \ --numRandomMarkerforVarianceRatio=1000
Please feel free to comment what the issues could be and about my code. Thank you!