error message fix?

[gradsmjin814]

1.00000000 0.02996877 Fixed-effect coefficients: [,1] [1,] -3.14901614 [2,] -0.07995703 [3,] 0.57563305 [4,] 0.04271480 [5,] -0.06675162 [6,] -0.05086717 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996877 Fixed-effect coefficients: [,1] [1,] -3.14901614 [2,] -0.07995703 [3,] 0.57563305 [4,] 0.04271480 [5,] -0.06675162 [6,] -0.05086717 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996902 Fixed-effect coefficients: [,1] [1,] -3.14901543 [2,] -0.07995704 [3,] 0.57563329 [4,] 0.04271486 [5,] -0.06675162 [6,] -0.05086723 [7,] 0.08083243 dim(X1): 2954 7 length(V): 2954 [1] 0 [1] 104001 iGet_Coef: 1 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 96133 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996902 Fixed-effect coefficients: [,1] iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996902 Fixed-effect coefficients: [,1] [1,] -3.14901543 [2,] -0.07995704 [3,] 0.57563329 [4,] 0.04271486 [5,] -0.06675162 [6,] -0.05086723 [7,] 0.08083243 dim(X1): 2954 7 length(V): 2954 [1] 0 [1] 104001 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996902 Fixed-effect coefficients: [,1] [1,] -3.14901543 [2,] -0.07995704 [3,] 0.57563329 [4,] 0.04271486 [5,] -0.06675162 [6,] -0.05086723 [7,] 0.08083243 dim(X1): 2954 7 length(V): 2954 [1] 0 [1] 104001 iGet_Coef: 1 Tau: [1] 1.00000000 0.04412649 Fixed-effect coefficients: [,1] [1,] -3.15879154 [2,] -0.08020736 [3,] 0.57776868 [4,] 0.04223903 [5,] -0.06733391 [6,] -0.05061452 [7,] 0.08098885 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996921 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996921 Fixed-effect coefficients: [,1] [1,] -3.14901710 [2,] -0.07995700 [3,] 0.57563293 [4,] 0.04271477 [5,] -0.06675161 [6,] -0.05086716 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996921 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996921 Fixed-effect coefficients: [,1] [1,] -3.14901710 [2,] -0.07995700 [3,] 0.57563293 [4,] 0.04271477 [5,] -0.06675161 [6,] -0.05086716 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996921 [1] 1

$SPAcutoff [1] 2

$numRandomMarkerforVarianceRatio [1] 30 [1] 1

$SPAcutoff [1] 2

$numRandomMarkerforVarianceRatio [1] 30

$skipModelFitting [1] FALSE

$memoryChunk [1] 2

$tauInit [1] "0,0" [1] 1

$SPAcutoff [1] 2

$numRandomMarkerforVarianceRatio [1] 30

$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

$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

$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

$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

iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.03919787 Fixed-effect coefficients: [,1] Tau: [1] 1.00000000 0.02996839 Fixed-effect coefficients: [,1] [1,] -3.14499378 [2,] -0.07967594 [3,] 0.57530946 [4,] 0.04358608 [5,] -0.06617837 [6,] -0.05155627 [7,] 0.08124178 [1] "OK" dim(X1): 2954 7 length(V): 2954 [1] 104002 [1] 204864 iGet_Coef: 1 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Msub_MAFge_minMAFtoConstructGRM 99693 iter from getPCG1ofSigmaAndVector 3 Tau: [1] 1.00000000 0.02996839 Fixed-effect coefficients: [,1] [1,] -3.14341974 [2,] -0.07986289 [3,] 0.57376480 [4,] 0.04282629 [5,] -0.06689128 [6,] -0.05123434 [7,] 0.08043773 [1] "OK" dim(X1): 2954 7 length(V): 2954 user system elapsed 5307.596 1404.601 106.746 t_end - t_begin, fitting the NULL model took user system elapsed 5304.580 1397.421 105.557 Start estimating variance ratios

Family: binomial Link function: logit

[1] FALSE dim(Rmat): 2954 39 dim(sqrtWinvN): 2954 2954 dim(sqrtWinvNR): 2954 39 dim(Dinv): 39 39 dim(RNWNR): 39 39 dim(ACm): 39 39 dim(WinvN): 2954 2954 dim(Rmat): 2954 39 dim(WinvNRt): 2954 39 dim(ACinv): 39 39 Only one variance ratio will be estimated using randomly selected markers with MAC >= 20 [1] "HERE6" pcg did not converge. You may increase maxiter number. iter from getPCG1ofSigmaAndVector 500 iter from getPCG1ofSigmaAndVector 138 iter from getPCG1ofSigmaAndVector 350 pcg did not converge. You may increase maxiter number. iter from getPCG1ofSigmaAndVector 500 pcg did not converge. You may increase maxiter number. iter from getPCG1ofSigmaAndVector 500 iter from getPCG1ofSigmaAndVector 132 iter from getPCG1ofSigmaAndVector 197 74516 th marker G0 1 1 0 1 2 2 0 0 1 2 pcg did not converge. You may increase maxiter number. iter from getPCG1ofSigmaAndVector 500 iter from getPCG1ofSigmaAndVector 54 iter from getPCG1ofSigmaAndVector 239 iter from getPCG1ofSigmaAndVector 362 iter from getPCG1ofSigmaAndVector 60 iter from getPCG1ofSigmaAndVector 445 iter from getPCG1ofSigmaAndVector 461 iter from getPCG1ofSigmaAndVector 243 Error in solve.default(t(X1) %*% Sigma_iX) : system is computationally singular: reciprocal condition number = 0 Calls: fitNULLGLMM ... scoreTest_SPAGMMAT_forVarianceRatio_binaryTrait -> solve -> solve -> solve.default Execution halted

this is the code I used

step1_fitNULLGLMM.R \ --plinkFile=$genPath/SWE_GSA/SWE_GSA_pi_case_noOverlapOE_QC_auto_2122 \ --phenoFile=$phenoCovarPath/phenoCovar_YAOSP_GSA_GWSS_240511.txt \ --phenoCol=Status \ --covarColList=YOB,SEX,AAO,PC1,PC2,PC3,PC4 \ --eventTimeCol=YAOSP \ --sampleIDColinphenoFile=MMSID \ --traitType=survival \ --outputPrefix=$outPath_test/YAOSP_GSA_240511 \ --nThreads=5 \ --LOCO=TRUE \ --minMAFforGRM=0.01 \ --skipModelFitting=FALSE \ --tauInit=1,0 \ --pcgforUhatforSurvAnalysis=FALSE \ --numRandomMarkerforVarianceRatio=1000

how can I fix it from here?