******************************************************************* * Genome-wide Complex Trait Analysis (GCTA) * version 1.94.0 beta Linux * (C) 2010-present, Jian Yang, The University of Queensland * Please report bugs to Jian Yang ******************************************************************* Analysis started at 21:40:29 +07 on Fri Nov 18 2022. Hostname: mga-mga.mga.local Options: --grm-sparse /home/freydin/GRM/ukb_ea_sp --fastGWA-mlm-binary --bfile /home/common/DataStorage/UKBB/Project_18219/ukb23155_v1/merge/exome_merge --autosome --threads 10 --maf 0.000005 --geno 0.02 --pheno /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/M54_self-rep_eur_gcta.txt --covar /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/M54_M51_bcovar_sex_batch_self-rep_eur_gcta.txt --qcovar /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/M54_M51_qcovar_pc1_10_age_self-rep_eur_gcta.txt --out /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/no_filters/exomes/M54/M54_self-rep_eur_exomes The program will be running with up to 10 threads. Reading PLINK FAM file from [/home/common/DataStorage/UKBB/Project_18219/ukb23155_v1/merge/exome_merge.fam]... 200643 individuals to be included from FAM file. Reading phenotype data from [/home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/M54_self-rep_eur_gcta.txt]... 187710 overlapping individuals with non-missing data to be included from the phenotype file. 187710 individuals to be included. 84186 males, 103524 females, 0 unknown. Reading PLINK BIM file from [/home/common/DataStorage/UKBB/Project_18219/ukb23155_v1/merge/exome_merge.bim]... 17981897 SNPs to be included from BIM file(s). 17549650 SNPs to be included on valid chromosomes Threshold to filter variants: MAF > 0.000005, missingness rate < 0.020000. Reading quantitative covariates from [/home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/M54_M51_qcovar_pc1_10_age_self-rep_eur_gcta.txt]. 11 covariates of 459161 samples to be included. Reading discrete covariates from [/home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/M54_M51_bcovar_sex_batch_self-rep_eur_gcta.txt]. 2 covariates of 459161 samples to be included. 11 qcovar, 2 covar and 0 rcovar to be included. 459161 common individuals among the covariate files to be included. 187710 overlapping individuals with non-missing data to be included from the covariate file(s). Reading the sparse GRM file from [/home/freydin/GRM/ukb_ea_sp]... After matching all the files, 183652 individuals to be included in the analysis. Performing GLM to get the starting values of beta for the covariates... GLM finished, fixed effects: 0.0104405 0.00448379 0.00623918 0.00540477 0.00538068 0.00538354 -0.00374794 -0.00654155 0.00277624 0.0134242 0.0147323 0.157842 0.227562 -4.18635 Initial Var(Y): 31.2157 Initializing with tao: 0, Var(Y): 31.21570, fixed effects: 0.0104405 0.00448379 0.00623918 0.00540477 0.00538068 0.00538354 -0.00374794 -0.00654155 0.00277624 0.0134242 0.0147323 0.157842 0.227562 -4.18635. ------------------------------------ Fine tuning within 0 ~ 31.5279 with 801 steps. Iteration 1, step size: 0.0394098, logL: -406798. Tao: 0, searching range: 0 to 0.0394098 Iteration 2, step size: 0.00262732, logL: -406798. Tao: 0.0183913, searching range: 0.0157639 to 0.0210186 Iteration 3, step size: 0.00035031, logL: -406798. Tao: 0.0189167, searching range: 0.0185664 to 0.019267 Iteration 4, step size: 4.67079e-05, logL: -406798. Tao: 0.0189401, searching range: 0.0188934 to 0.0189868 Iteration 5, step size: 6.22773e-06, logL: -406798. Tao: 0.0189494, searching range: 0.0189432 to 0.0189556 Iteration 6, step size: 8.30363e-07, logL: -406798. Tao: 0.0189465, searching range: 0.0189457 to 0.0189473 Iteration 7, step size: 1.10715e-07, logL: -406798. Tao: 0.0189467, searching range: 0.0189466 to 0.0189468 Iter 0, tao: 0.0189467, Var(Y): 30.2045, fixed effects: 0.0104413 0.004485 0.00623831 0.00540499 0.00538047 0.00538352 -0.00374721 -0.0065404 0.00277651 0.0134248 0.0147321 0.157842 0.227566 -4.18634. ------------------------------------ Fine tuning within 0 ~ 0.189467 with 201 steps. Iteration 1, step size: 0.000947334, logL: -405303. Tao: 0.0189467, searching range: 0.0179993 to 0.019894 Iteration 2, step size: 0.000126311, logL: -405303. Tao: 0.0185046, searching range: 0.0183783 to 0.0186309 Iteration 3, step size: 1.68415e-05, logL: -405303. Tao: 0.018513, searching range: 0.0184962 to 0.0185298 Iteration 4, step size: 2.24553e-06, logL: -405303. Tao: 0.0185119, searching range: 0.0185096 to 0.0185141 Iteration 5, step size: 2.99404e-07, logL: -405303. Tao: 0.0185099, searching range: 0.0185096 to 0.0185102 Iteration 6, step size: 3.99206e-08, logL: -405303. Tao: 0.01851, searching range: 0.0185099 to 0.01851 Iteration 7, step size: 5.32274e-09, logL: -405303. Tao: 0.01851, searching range: 0.01851 to 0.01851 Iter 1, tao: 0.01851, Var(Y): 30.2277, fixed effects: 0.0104413 0.00448496 0.00623831 0.00540497 0.00538044 0.00538349 -0.0037472 -0.00654039 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Fine tuning within 0 ~ 0.1851 with 201 steps. Iteration 1, step size: 0.000925498, logL: -405338. Tao: 0.01851, searching range: 0.0175845 to 0.0194355 Iteration 2, step size: 0.0001234, logL: -405338. Tao: 0.0186951, searching range: 0.0185717 to 0.0188185 Iteration 3, step size: 1.64533e-05, logL: -405338. Tao: 0.0186704, searching range: 0.0186539 to 0.0186868 Iteration 4, step size: 2.19377e-06, logL: -405338. Tao: 0.0186605, searching range: 0.0186583 to 0.0186627 Iteration 5, step size: 2.92503e-07, logL: -405338. Tao: 0.0186621, searching range: 0.0186618 to 0.0186624 Iteration 6, step size: 3.90004e-08, logL: -405338. Tao: 0.0186624, searching range: 0.0186623 to 0.0186624 Iteration 7, step size: 5.20006e-09, logL: -405338. Tao: 0.0186624, searching range: 0.0186624 to 0.0186624 Iter 2, tao: 0.0186624, Var(Y): 30.2197, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Mean tao in first 3 iterations: 0.0187063. Fine tuning within 0 ~ 0.022736 . Iteration 1, step size: 0.00045472, logL: -405326. Tao: 0.0186435, searching range: 0.0181888 to 0.0190982 Iteration 2, step size: 6.06294e-05, logL: -405326. Tao: 0.0186738, searching range: 0.0186132 to 0.0187345 Iteration 3, step size: 8.08391e-06, logL: -405326. Tao: 0.0186617, searching range: 0.0186536 to 0.0186698 Iteration 4, step size: 1.07786e-06, logL: -405326. Tao: 0.0186644, searching range: 0.0186633 to 0.0186655 Iteration 5, step size: 1.43714e-07, logL: -405326. Tao: 0.0186652, searching range: 0.0186651 to 0.0186653 Iteration 6, step size: 1.91619e-08, logL: -405326. Tao: 0.0186651, searching range: 0.0186651 to 0.0186652 Iteration 7, step size: 2.55492e-09, logL: -405326. Tao: 0.0186651, searching range: 0.0186651 to 0.0186651 Iter 3, tao: 0.0186651, Var(Y): 30.2195, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Iteration 1, step size: 0.00045472, logL: -405326. Tao: 0.0186435, searching range: 0.0181888 to 0.0190982 Iteration 2, step size: 6.06294e-05, logL: -405326. Tao: 0.0186738, searching range: 0.0186132 to 0.0187345 Iteration 3, step size: 8.08391e-06, logL: -405326. Tao: 0.0186617, searching range: 0.0186536 to 0.0186698 Iteration 4, step size: 1.07786e-06, logL: -405326. Tao: 0.0186579, searching range: 0.0186569 to 0.018659 Iteration 5, step size: 1.43714e-07, logL: -405326. Tao: 0.018657, searching range: 0.0186569 to 0.0186572 Iteration 6, step size: 1.91619e-08, logL: -405326. Tao: 0.018657, searching range: 0.018657 to 0.018657 Iteration 7, step size: 2.55492e-09, logL: -405326. Tao: 0.018657, searching range: 0.018657 to 0.018657 Iter 4, tao: 0.018657, Var(Y): 30.2199, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Iteration 1, step size: 0.00045472, logL: -405326. Tao: 0.0186435, searching range: 0.0181888 to 0.0190982 Iteration 2, step size: 6.06294e-05, logL: -405326. Tao: 0.0186738, searching range: 0.0186132 to 0.0187345 Iteration 3, step size: 8.08391e-06, logL: -405326. Tao: 0.0186617, searching range: 0.0186536 to 0.0186698 Iteration 4, step size: 1.07786e-06, logL: -405326. Tao: 0.0186644, searching range: 0.0186633 to 0.0186655 Iteration 5, step size: 1.43714e-07, logL: -405326. Tao: 0.0186643, searching range: 0.0186642 to 0.0186645 Iteration 6, step size: 1.91619e-08, logL: -405326. Tao: 0.0186643, searching range: 0.0186643 to 0.0186644 Iteration 7, step size: 2.55492e-09, logL: -405326. Tao: 0.0186644, searching range: 0.0186644 to 0.0186644 Iter 5, tao: 0.0186644, Var(Y): 30.2196, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Iteration 1, step size: 0.00045472, logL: -405326. Tao: 0.0186435, searching range: 0.0181888 to 0.0190982 Iteration 2, step size: 6.06294e-05, logL: -405326. Tao: 0.0186738, searching range: 0.0186132 to 0.0187345 Iteration 3, step size: 8.08391e-06, logL: -405326. Tao: 0.0186536, searching range: 0.0186455 to 0.0186617 Iteration 4, step size: 1.07786e-06, logL: -405326. Tao: 0.0186585, searching range: 0.0186574 to 0.0186596 Iteration 5, step size: 1.43714e-07, logL: -405326. Tao: 0.0186587, searching range: 0.0186586 to 0.0186588 Iteration 6, step size: 1.91619e-08, logL: -405326. Tao: 0.0186588, searching range: 0.0186588 to 0.0186588 Iteration 7, step size: 2.55492e-09, logL: -405326. Tao: 0.0186588, searching range: 0.0186588 to 0.0186588 Iter 6, tao: 0.0186588, Var(Y): 30.2199, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Mean tao in past 3 iterations: 0.01866. Fine tuning within 0 ~ 0.0223972 . Iteration 1, step size: 0.000447945, logL: -405326. Tao: 0.0188137, searching range: 0.0183657 to 0.0192616 Iteration 2, step size: 5.9726e-05, logL: -405326. Tao: 0.0186644, searching range: 0.0186046 to 0.0187241 Iteration 3, step size: 7.96346e-06, logL: -405326. Tao: 0.0186604, searching range: 0.0186524 to 0.0186683 Iteration 4, step size: 1.06179e-06, logL: -405326. Tao: 0.0186652, searching range: 0.0186641 to 0.0186662 Iteration 5, step size: 1.41573e-07, logL: -405326. Tao: 0.0186655, searching range: 0.0186654 to 0.0186657 Iteration 6, step size: 1.88764e-08, logL: -405326. Tao: 0.0186655, searching range: 0.0186655 to 0.0186655 Iteration 7, step size: 2.51685e-09, logL: -405326. Tao: 0.0186655, searching range: 0.0186655 to 0.0186655 Iter 7, tao: 0.0186655, Var(Y): 30.2195, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Mean tao in past 3 iterations: 0.0186629. Fine tuning within 0 ~ 0.0223986 . Iteration 1, step size: 0.000447973, logL: -405326. Tao: 0.0188148, searching range: 0.0183669 to 0.0192628 Iteration 2, step size: 5.97297e-05, logL: -405326. Tao: 0.0186655, searching range: 0.0186058 to 0.0187253 Iteration 3, step size: 7.96396e-06, logL: -405326. Tao: 0.0186615, searching range: 0.0186536 to 0.0186695 Iteration 4, step size: 1.06186e-06, logL: -405326. Tao: 0.0186568, searching range: 0.0186557 to 0.0186578 Iteration 5, step size: 1.41581e-07, logL: -405326. Tao: 0.0186571, searching range: 0.018657 to 0.0186573 Iteration 6, step size: 1.88775e-08, logL: -405326. Tao: 0.018657, searching range: 0.018657 to 0.0186571 Iteration 7, step size: 2.517e-09, logL: -405326. Tao: 0.018657, searching range: 0.018657 to 0.018657 Iter 8, tao: 0.018657, Var(Y): 30.2199, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Mean tao in past 3 iterations: 0.0186605. Fine tuning within 0 ~ 0.0223986 . Iteration 1, step size: 0.000447973, logL: -405326. Tao: 0.0188148, searching range: 0.0183669 to 0.0192628 Iteration 2, step size: 5.97297e-05, logL: -405326. Tao: 0.0186655, searching range: 0.0186058 to 0.0187253 Iteration 3, step size: 7.96396e-06, logL: -405326. Tao: 0.0186615, searching range: 0.0186536 to 0.0186695 Iteration 4, step size: 1.06186e-06, logL: -405326. Tao: 0.0186631, searching range: 0.0186621 to 0.0186642 Iteration 5, step size: 1.41581e-07, logL: -405326. Tao: 0.0186625, searching range: 0.0186624 to 0.0186626 Iteration 6, step size: 1.88775e-08, logL: -405326. Tao: 0.0186626, searching range: 0.0186626 to 0.0186626 Iteration 7, step size: 2.517e-09, logL: -405326. Tao: 0.0186626, searching range: 0.0186626 to 0.0186626 Iter 9, tao: 0.0186626, Var(Y): 30.2197, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. ------------------------------------ Mean tao in past 3 iterations: 0.0186617. Fine tuning within 0 ~ 0.0223986 . Iteration 1, step size: 0.000447973, logL: -405326. Tao: 0.0188148, searching range: 0.0183669 to 0.0192628 Iteration 2, step size: 5.97297e-05, logL: -405326. Tao: 0.0186655, searching range: 0.0186058 to 0.0187253 Iteration 3, step size: 7.96396e-06, logL: -405326. Tao: 0.0186615, searching range: 0.0186536 to 0.0186695 Iteration 4, step size: 1.06186e-06, logL: -405326. Tao: 0.0186631, searching range: 0.0186621 to 0.0186642 Iteration 5, step size: 1.41581e-07, logL: -405326. Tao: 0.0186633, searching range: 0.0186632 to 0.0186635 Iteration 6, step size: 1.88775e-08, logL: -405326. Tao: 0.0186634, searching range: 0.0186634 to 0.0186634 Iteration 7, step size: 2.517e-09, logL: -405326. Tao: 0.0186634, searching range: 0.0186634 to 0.0186634 Iter 10, tao: 0.0186634, Var(Y): 30.2196, fixed effects: 0.0104413 0.00448497 0.0062383 0.00540497 0.00538044 0.00538349 -0.00374719 -0.00654038 0.00277649 0.0134248 0.014732 0.157841 0.227565 -4.18634. fastGWA-BB-REML converged. fastGWA-BB-REML finished in 669.741 seconds. Tuning parameters using null SNPs... reading 200 SNP... 100% finished in 1.7 sec 200 SNPs have been processed. Not enough null SNPs. reading 200 SNP... 100% finished in 1.7 sec 200 SNPs have been processed. Mean GRAMMAR-Gamma value = 0.999232 Tuning time: 3.3994 seconds. Performing fastGWA generalized linear mixed model association analysis... fastGWA results will be saved in text format to [/home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/no_filters/exomes/M54/M54_self-rep_eur_exomes.fastGWA]. 1.8% Estimated time remaining 278.9 min 3.6% Estimated time remaining 267.5 min 5.5% Estimated time remaining 259.7 min 7.4% Estimated time remaining 253.0 min 9.3% Estimated time remaining 246.2 min 11.3% Estimated time remaining 240.2 min 13.3% Estimated time remaining 234.2 min 15.2% Estimated time remaining 228.5 min 17.2% Estimated time remaining 222.8 min 19.0% Estimated time remaining 217.7 min 21.0% Estimated time remaining 212.3 min 23.0% Estimated time remaining 206.8 min 24.8% Estimated time remaining 201.8 min 26.8% Estimated time remaining 196.3 min 28.8% Estimated time remaining 190.9 min 30.7% Estimated time remaining 185.5 min 32.6% Estimated time remaining 180.5 min 34.5% Estimated time remaining 175.2 min 36.5% Estimated time remaining 169.8 min 38.4% Estimated time remaining 164.9 min 40.2% Estimated time remaining 160.0 min 42.1% Estimated time remaining 154.9 min 44.1% Estimated time remaining 149.7 min 46.0% Estimated time remaining 144.4 min 48.0% Estimated time remaining 139.2 min 49.9% Estimated time remaining 134.2 min 51.7% Estimated time remaining 129.3 min 53.7% Estimated time remaining 124.0 min 55.5% Estimated time remaining 119.0 min 57.5% Estimated time remaining 113.8 min 59.5% Estimated time remaining 108.5 min 61.3% Estimated time remaining 103.5 min 63.3% Estimated time remaining 98.2 min 65.3% Estimated time remaining 93.0 min 67.1% Estimated time remaining 88.0 min 69.1% Estimated time remaining 82.7 min 71.0% Estimated time remaining 77.7 min 72.9% Estimated time remaining 72.5 min 74.8% Estimated time remaining 67.5 min 76.6% Estimated time remaining 62.5 min 78.5% Estimated time remaining 57.5 min 80.4% Estimated time remaining 52.5 min 82.3% Estimated time remaining 47.3 min 84.3% Estimated time remaining 42.0 min 86.2% Estimated time remaining 37.0 min 88.0% Estimated time remaining 32.0 min 89.9% Estimated time remaining 27.0 min 91.8% Estimated time remaining 22.0 min 93.6% Estimated time remaining 17.0 min 95.6% Estimated time remaining 11.8 min 97.5% Estimated time remaining 6.8 min 99.3% Estimated time remaining 1.8 min 100% finished in 16085.9 sec 17549650 SNPs have been processed. Saved 7998110 SNPs. Analysis finished at 02:20:26 +07 on Sat Nov 19 2022 Overall computational time: 4 hours 39 minutes 56 sec.