******************************************************************* * 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 21:36:20 +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/M51_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/M51/M51_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/M51_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: 0.00594769 0.00595249 -0.006399 0.000128521 -0.000702224 -0.00320412 0.0034501 -0.00265656 0.0013207 0.0100792 0.00407722 0.12836 0.279584 -4.31486 Initial Var(Y): 59.2363 Initializing with tao: 0, Var(Y): 59.23630, fixed effects: 0.00594769 0.00595249 -0.006399 0.000128521 -0.000702224 -0.00320412 0.0034501 -0.00265656 0.0013207 0.0100792 0.00407722 0.12836 0.279584 -4.31486. ------------------------------------ Fine tuning within 0 ~ 59.8286 with 801 steps. Iteration 1, step size: 0.0747858, logL: -466283. Tao: 0, searching range: 0 to 0.0747858 Iteration 2, step size: 0.00498572, logL: -466283. Tao: 0.0349, searching range: 0.0299143 to 0.0398857 Iteration 3, step size: 0.000664762, logL: -466283. Tao: 0.0332381, searching range: 0.0325734 to 0.0339029 Iteration 4, step size: 8.8635e-05, logL: -466283. Tao: 0.0332824, searching range: 0.0331938 to 0.0333711 Iteration 5, step size: 1.1818e-05, logL: -466283. Tao: 0.0332529, searching range: 0.0332411 to 0.0332647 Iteration 6, step size: 1.57573e-06, logL: -466283. Tao: 0.033249, searching range: 0.0332474 to 0.0332505 Iteration 7, step size: 2.10098e-07, logL: -466283. Tao: 0.0332488, searching range: 0.0332486 to 0.0332491 Iter 0, tao: 0.0332488, Var(Y): 55.6838, fixed effects: 0.00594976 0.00595333 -0.00639989 0.000129174 -0.000702129 -0.00320283 0.00345091 -0.00265702 0.00132128 0.0100807 0.0040773 0.128358 0.279585 -4.31485. ------------------------------------ Fine tuning within 0 ~ 0.332488 with 201 steps. Iteration 1, step size: 0.00166244, logL: -463489. Tao: 0.0315864, searching range: 0.029924 to 0.0332488 Iteration 2, step size: 0.000221659, logL: -463489. Tao: 0.0319189, searching range: 0.0316972 to 0.0321406 Iteration 3, step size: 2.95545e-05, logL: -463489. Tao: 0.0318155, searching range: 0.0317859 to 0.031845 Iteration 4, step size: 3.9406e-06, logL: -463489. Tao: 0.0318135, searching range: 0.0318095 to 0.0318174 Iteration 5, step size: 5.25414e-07, logL: -463489. Tao: 0.0318132, searching range: 0.0318127 to 0.0318137 Iteration 6, step size: 7.00552e-08, logL: -463489. Tao: 0.0318137, searching range: 0.0318137 to 0.0318137 Iteration 7, step size: 4.67035e-09, logL: -463489. Tao: 0.0318137, searching range: 0.0318137 to 0.0318137 Iter 1, tao: 0.0318137, Var(Y): 55.8333, fixed effects: 0.00594963 0.00595325 -0.00639981 0.000129149 -0.000702123 -0.00320285 0.00345086 -0.00265698 0.00132125 0.0100806 0.00407727 0.128357 0.279582 -4.31485. ------------------------------------ Fine tuning within 0 ~ 0.318137 with 201 steps. Iteration 1, step size: 0.00159069, logL: -463609. Tao: 0.0318137, searching range: 0.0302231 to 0.0334044 Iteration 2, step size: 0.000212092, logL: -463609. Tao: 0.032344, searching range: 0.0321319 to 0.0325561 Iteration 3, step size: 2.82789e-05, logL: -463609. Tao: 0.0323016, searching range: 0.0322733 to 0.0323298 Iteration 4, step size: 3.77052e-06, logL: -463609. Tao: 0.0323034, searching range: 0.0322997 to 0.0323072 Iteration 5, step size: 5.02736e-07, logL: -463609. Tao: 0.0323067, searching range: 0.0323062 to 0.0323072 Iteration 6, step size: 6.70314e-08, logL: -463609. Tao: 0.0323066, searching range: 0.0323065 to 0.0323067 Iteration 7, step size: 8.93752e-09, logL: -463609. Tao: 0.0323067, searching range: 0.0323067 to 0.0323067 Iter 2, tao: 0.0323067, Var(Y): 55.7822, fixed effects: 0.00594966 0.00595326 -0.00639982 0.000129159 -0.000702121 -0.00320283 0.00345087 -0.00265698 0.00132126 0.0100806 0.00407727 0.128357 0.279582 -4.31485. ------------------------------------ Mean tao in first 3 iterations: 0.0324564. Fine tuning within 0 ~ 0.0398986 . Iteration 1, step size: 0.000797972, logL: -463569. Tao: 0.0319189, searching range: 0.0311209 to 0.0327169 Iteration 2, step size: 0.000106396, logL: -463569. Tao: 0.0322913, searching range: 0.0321849 to 0.0323977 Iteration 3, step size: 1.41862e-05, logL: -463569. Tao: 0.0322984, searching range: 0.0322842 to 0.0323126 Iteration 4, step size: 1.89149e-06, logL: -463569. Tao: 0.0322918, searching range: 0.0322899 to 0.0322936 Iteration 5, step size: 2.52199e-07, logL: -463569. Tao: 0.0322914, searching range: 0.0322911 to 0.0322916 Iteration 6, step size: 3.36265e-08, logL: -463569. Tao: 0.0322915, searching range: 0.0322915 to 0.0322915 Iteration 7, step size: 4.48353e-09, logL: -463569. Tao: 0.0322915, searching range: 0.0322915 to 0.0322915 Iter 3, tao: 0.0322915, Var(Y): 55.7838, fixed effects: 0.00594966 0.00595326 -0.00639982 0.000129159 -0.000702121 -0.00320283 0.00345087 -0.00265698 0.00132126 0.0100806 0.00407727 0.128357 0.279582 -4.31485. ------------------------------------ Iteration 1, step size: 0.000797972, logL: -463570. Tao: 0.0319189, searching range: 0.0311209 to 0.0327169 Iteration 2, step size: 0.000106396, logL: -463570. Tao: 0.0322913, searching range: 0.0321849 to 0.0323977 Iteration 3, step size: 1.41862e-05, logL: -463570. Tao: 0.0322984, searching range: 0.0322842 to 0.0323126 Iteration 4, step size: 1.89149e-06, logL: -463570. Tao: 0.0323031, searching range: 0.0323012 to 0.032305 Iteration 5, step size: 2.52199e-07, logL: -463570. Tao: 0.0323032, searching range: 0.032303 to 0.0323035 Iteration 6, step size: 3.36265e-08, logL: -463570. Tao: 0.0323034, searching range: 0.0323034 to 0.0323035 Iteration 7, step size: 4.48353e-09, logL: -463570. Tao: 0.0323035, searching range: 0.0323035 to 0.0323035 Iter 4, tao: 0.0323035, Var(Y): 55.7826, fixed effects: 0.00594966 0.00595326 -0.00639982 0.000129159 -0.000702121 -0.00320283 0.00345087 -0.00265698 0.00132126 0.0100806 0.00407727 0.128357 0.279582 -4.31485. ------------------------------------ Iteration 1, step size: 0.000797972, logL: -463569. Tao: 0.0319189, searching range: 0.0311209 to 0.0327169 Iteration 2, step size: 0.000106396, logL: -463569. Tao: 0.0322913, searching range: 0.0321849 to 0.0323977 Iteration 3, step size: 1.41862e-05, logL: -463569. Tao: 0.0323126, searching range: 0.0322984 to 0.0323267 Iteration 4, step size: 1.89149e-06, logL: -463569. Tao: 0.0323116, searching range: 0.0323097 to 0.0323135 Iteration 5, step size: 2.52199e-07, logL: -463569. Tao: 0.0323125, searching range: 0.0323122 to 0.0323127 Iteration 6, step size: 3.36265e-08, logL: -463569. Tao: 0.0323124, searching range: 0.0323124 to 0.0323125 Iteration 7, step size: 4.48353e-09, logL: -463569. Tao: 0.0323124, searching range: 0.0323124 to 0.0323124 Iter 5, tao: 0.0323124, Var(Y): 55.7816, fixed effects: 0.00594966 0.00595326 -0.00639982 0.000129159 -0.000702121 -0.00320283 0.00345087 -0.00265699 0.00132126 0.0100806 0.00407727 0.128357 0.279582 -4.31485. ------------------------------------ Iteration 1, step size: 0.000797972, logL: -463568. Tao: 0.0319189, searching range: 0.0311209 to 0.0327169 Iteration 2, step size: 0.000106396, logL: -463568. Tao: 0.0322913, searching range: 0.0321849 to 0.0323977 Iteration 3, step size: 1.41862e-05, logL: -463568. Tao: 0.0322984, searching range: 0.0322842 to 0.0323126 Iteration 4, step size: 1.89149e-06, logL: -463568. Tao: 0.0323069, searching range: 0.032305 to 0.0323088 Iteration 5, step size: 2.52199e-07, logL: -463568. Tao: 0.0323085, searching range: 0.0323083 to 0.0323088 Iteration 6, step size: 3.36265e-08, logL: -463568. Tao: 0.0323087, searching range: 0.0323087 to 0.0323088 Iteration 7, step size: 4.48353e-09, logL: -463568. Tao: 0.0323087, searching range: 0.0323087 to 0.0323087 Iter 6, tao: 0.0323087, Var(Y): 55.782, fixed effects: 0.00594966 0.00595326 -0.00639982 0.000129159 -0.000702121 -0.00320283 0.00345087 -0.00265698 0.00132126 0.0100806 0.00407727 0.128357 0.279582 -4.31485. ------------------------------------ Mean tao in past 3 iterations: 0.0323082. Fine tuning within 0 ~ 0.0387749 . Iteration 1, step size: 0.000775498, logL: -463569. Tao: 0.0325709, searching range: 0.0317954 to 0.0333464 Iteration 2, step size: 0.0001034, logL: -463569. Tao: 0.0323124, searching range: 0.032209 to 0.0324158 Iteration 3, step size: 1.37866e-05, logL: -463569. Tao: 0.0323055, searching range: 0.0322917 to 0.0323193 Iteration 4, step size: 1.83822e-06, logL: -463569. Tao: 0.0323065, searching range: 0.0323046 to 0.0323083 Iteration 5, step size: 2.45096e-07, logL: -463569. Tao: 0.032308, searching range: 0.0323078 to 0.0323083 Iteration 6, step size: 3.26794e-08, logL: -463569. Tao: 0.0323082, searching range: 0.0323082 to 0.0323082 Iteration 7, step size: 4.35726e-09, logL: -463569. Tao: 0.0323082, searching range: 0.0323082 to 0.0323082 Iter 7, tao: 0.0323082, Var(Y): 55.7821, fixed effects: 0.00594966 0.00595326 -0.00639982 0.000129159 -0.000702121 -0.00320283 0.00345087 -0.00265698 0.00132126 0.0100806 0.00407727 0.128357 0.279582 -4.31485. fastGWA-BB-REML converged. fastGWA-BB-REML finished in 889.537 seconds. Tuning parameters using null SNPs... reading 200 SNP... 100% finished in 6.9 sec 200 SNPs have been processed. Not enough null SNPs. reading 200 SNP... 100% finished in 6.9 sec 200 SNPs have been processed. Mean GRAMMAR-Gamma value = 0.999311 Tuning time: 13.7805 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/M51/M51_self-rep_eur_exomes.fastGWA]. 1.5% Estimated time remaining 351.6 min 3.0% Estimated time remaining 342.7 min 4.4% Estimated time remaining 343.2 min 5.8% Estimated time remaining 341.5 min 7.2% Estimated time remaining 338.1 min 8.6% Estimated time remaining 333.7 min 10.0% Estimated time remaining 328.7 min 11.5% Estimated time remaining 320.6 min 13.1% Estimated time remaining 311.8 min 14.6% Estimated time remaining 304.6 min 16.1% Estimated time remaining 298.2 min 17.6% Estimated time remaining 293.0 min 19.0% Estimated time remaining 286.9 min 20.5% Estimated time remaining 281.2 min 22.0% Estimated time remaining 275.8 min 23.5% Estimated time remaining 270.5 min 25.0% Estimated time remaining 264.4 min 26.6% Estimated time remaining 257.5 min 27.8% Estimated time remaining 255.4 min 29.4% Estimated time remaining 248.5 min 31.0% Estimated time remaining 241.8 min 32.6% Estimated time remaining 235.7 min 34.1% Estimated time remaining 230.2 min 35.7% Estimated time remaining 224.0 min 37.3% Estimated time remaining 217.7 min 38.8% Estimated time remaining 211.4 min 40.5% Estimated time remaining 204.9 min 42.1% Estimated time remaining 198.8 min 43.7% Estimated time remaining 192.8 min 45.4% Estimated time remaining 186.5 min 47.1% Estimated time remaining 180.2 min 48.6% Estimated time remaining 174.4 min 50.0% Estimated time remaining 170.2 min 51.7% Estimated time remaining 164.1 min 53.3% Estimated time remaining 158.4 min 54.9% Estimated time remaining 152.7 min 56.6% Estimated time remaining 146.6 min 58.2% Estimated time remaining 141.1 min 59.8% Estimated time remaining 135.1 min 61.4% Estimated time remaining 129.6 min 63.0% Estimated time remaining 124.1 min 64.6% Estimated time remaining 118.7 min 66.2% Estimated time remaining 113.3 min 67.8% Estimated time remaining 107.8 min 69.5% Estimated time remaining 102.0 min 71.0% Estimated time remaining 96.6 min 72.6% Estimated time remaining 91.2 min 74.1% Estimated time remaining 86.3 min 75.7% Estimated time remaining 81.0 min 77.3% Estimated time remaining 75.6 min 78.9% Estimated time remaining 70.3 min 80.4% Estimated time remaining 65.4 min 82.0% Estimated time remaining 60.0 min 83.6% Estimated time remaining 54.7 min 85.1% Estimated time remaining 49.4 min 86.7% Estimated time remaining 44.1 min 88.3% Estimated time remaining 38.8 min 89.9% Estimated time remaining 33.5 min 91.5% Estimated time remaining 28.2 min 93.1% Estimated time remaining 22.9 min 94.8% Estimated time remaining 17.3 min 96.4% Estimated time remaining 12.1 min 97.9% Estimated time remaining 6.8 min 99.5% Estimated time remaining 1.6 min 100% finished in 19849.7 sec 17549650 SNPs have been processed. Saved 7998110 SNPs. Analysis finished at 03:22:58 +07 on Sat Nov 19 2022 Overall computational time: 5 hours 46 minutes 38 sec.