******************************************************************* * 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 13:32:48 +07 on Sat Nov 19 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/CBP_self-rep_eur_gcta.txt --covar /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/CBP_bcovar_sex_batch_self-rep_eur_gcta.txt --qcovar /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/CBP_qcovar_pc1_10_age_self-rep_eur_gcta.txt --out /home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/no_filters/exomes/CBP/CBP_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/CBP_self-rep_eur_gcta.txt]... 182903 overlapping individuals with non-missing data to be included from the phenotype file. 182903 individuals to be included. 82403 males, 100500 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/CBP_qcovar_pc1_10_age_self-rep_eur_gcta.txt]. 11 covariates of 447466 samples to be included. Reading discrete covariates from [/home/common/projects/pain_project/fastGWA_mlm_binary_GWAS/CBP_bcovar_sex_batch_self-rep_eur_gcta.txt]. 2 covariates of 447466 samples to be included. 11 qcovar, 2 covar and 0 rcovar to be included. 447466 common individuals among the covariate files to be included. 182903 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, 178963 individuals to be included in the analysis. Performing GLM to get the starting values of beta for the covariates... GLM finished, fixed effects: 0.00287397 -0.00199444 -0.000115872 -0.000413622 0.000531702 0.00237986 -0.00231236 0.00347851 0.000579574 0.0108814 0.00507074 0.0382228 0.154266 -1.79707 Initial Var(Y): 6.82083 Initializing with tao: 0, Var(Y): 6.820830, fixed effects: 0.00287397 -0.00199444 -0.000115872 -0.000413622 0.000531702 0.00237986 -0.00231236 0.00347851 0.000579574 0.0108814 0.00507074 0.0382228 0.154266 -1.79707. ------------------------------------ Fine tuning within 0 ~ 6.88904 with 801 steps. Iteration 1, step size: 0.0086113, logL: -261252. Tao: 0.0172226, searching range: 0.0086113 to 0.0258339 Iteration 2, step size: 0.00114817, logL: -261252. Tao: 0.0166485, searching range: 0.0155003 to 0.0177967 Iteration 3, step size: 0.00015309, logL: -261252. Tao: 0.0168782, searching range: 0.0167251 to 0.0170312 Iteration 4, step size: 2.0412e-05, logL: -261252. Tao: 0.0168271, searching range: 0.0168067 to 0.0168475 Iteration 5, step size: 2.7216e-06, logL: -261252. Tao: 0.0168203, searching range: 0.0168176 to 0.016823 Iteration 6, step size: 3.6288e-07, logL: -261252. Tao: 0.0168201, searching range: 0.0168198 to 0.0168205 Iteration 7, step size: 4.83839e-08, logL: -261252. Tao: 0.0168198, searching range: 0.0168198 to 0.0168199 Iter 0, tao: 0.0168198, Var(Y): 6.72739, fixed effects: 0.00287462 -0.00199494 -0.000117314 -0.000413693 0.000531719 0.00237961 -0.00231263 0.00347665 0.000579545 0.0108795 0.00507102 0.0382235 0.154268 -1.79708. ------------------------------------ Fine tuning within 0 ~ 0.168198 with 201 steps. Iteration 1, step size: 0.000840991, logL: -260639. Tao: 0.0168198, searching range: 0.0159788 to 0.0176608 Iteration 2, step size: 0.000112132, logL: -260639. Tao: 0.0166516, searching range: 0.0165395 to 0.0167638 Iteration 3, step size: 1.4951e-05, logL: -260639. Tao: 0.016689, searching range: 0.0166741 to 0.016704 Iteration 4, step size: 1.99346e-06, logL: -260639. Tao: 0.01669, searching range: 0.016688 to 0.016692 Iteration 5, step size: 2.65795e-07, logL: -260639. Tao: 0.0166909, searching range: 0.0166907 to 0.0166912 Iteration 6, step size: 3.54393e-08, logL: -260639. Tao: 0.0166908, searching range: 0.0166908 to 0.0166909 Iteration 7, step size: 4.72524e-09, logL: -260639. Tao: 0.0166908, searching range: 0.0166908 to 0.0166908 Iter 1, tao: 0.0166908, Var(Y): 6.72822, fixed effects: 0.0028746 -0.00199493 -0.000117304 -0.000413687 0.000531721 0.0023796 -0.00231263 0.00347666 0.00057954 0.0108795 0.00507101 0.0382234 0.154268 -1.79709. ------------------------------------ Fine tuning within 0 ~ 0.166908 with 201 steps. Iteration 1, step size: 0.000834541, logL: -260645. Tao: 0.0166908, searching range: 0.0158563 to 0.0175254 Iteration 2, step size: 0.000111272, logL: -260645. Tao: 0.0167465, searching range: 0.0166352 to 0.0168577 Iteration 3, step size: 1.48363e-05, logL: -260645. Tao: 0.016739, searching range: 0.0167242 to 0.0167539 Iteration 4, step size: 1.97817e-06, logL: -260645. Tao: 0.016746, searching range: 0.016744 to 0.0167479 Iteration 5, step size: 2.63756e-07, logL: -260645. Tao: 0.0167458, searching range: 0.0167456 to 0.0167461 Iteration 6, step size: 3.51675e-08, logL: -260645. Tao: 0.016746, searching range: 0.016746 to 0.0167461 Iteration 7, step size: 4.689e-09, logL: -260645. Tao: 0.016746, searching range: 0.016746 to 0.016746 Iter 2, tao: 0.016746, Var(Y): 6.72791, fixed effects: 0.0028746 -0.00199493 -0.000117309 -0.000413687 0.000531721 0.0023796 -0.00231263 0.00347665 0.00057954 0.0108795 0.00507101 0.0382234 0.154268 -1.79709. ------------------------------------ Mean tao in first 3 iterations: 0.0167522. Fine tuning within 0 ~ 0.0201838 . Iteration 1, step size: 0.000403676, logL: -260644. Tao: 0.0165507, searching range: 0.016147 to 0.0169544 Iteration 2, step size: 5.38234e-05, logL: -260644. Tao: 0.0167391, searching range: 0.0166853 to 0.0167929 Iteration 3, step size: 7.17646e-06, logL: -260644. Tao: 0.0167499, searching range: 0.0167427 to 0.016757 Iteration 4, step size: 9.56861e-07, logL: -260644. Tao: 0.0167475, searching range: 0.0167465 to 0.0167484 Iteration 5, step size: 1.27581e-07, logL: -260644. Tao: 0.016748, searching range: 0.0167479 to 0.0167482 Iteration 6, step size: 1.70109e-08, logL: -260644. Tao: 0.0167481, searching range: 0.0167481 to 0.0167481 Iteration 7, step size: 2.26811e-09, logL: -260644. Tao: 0.0167481, searching range: 0.0167481 to 0.0167481 Iter 3, tao: 0.0167481, Var(Y): 6.7279, fixed effects: 0.0028746 -0.00199494 -0.000117309 -0.000413687 0.000531721 0.0023796 -0.00231263 0.00347665 0.00057954 0.0108795 0.00507101 0.0382234 0.154268 -1.79709. ------------------------------------ Iteration 1, step size: 0.000403676, logL: -260643. Tao: 0.0165507, searching range: 0.016147 to 0.0169544 Iteration 2, step size: 5.38234e-05, logL: -260643. Tao: 0.0167391, searching range: 0.0166853 to 0.0167929 Iteration 3, step size: 7.17646e-06, logL: -260643. Tao: 0.0167499, searching range: 0.0167427 to 0.016757 Iteration 4, step size: 9.56861e-07, logL: -260643. Tao: 0.0167484, searching range: 0.0167475 to 0.0167494 Iteration 5, step size: 1.27581e-07, logL: -260643. Tao: 0.0167481, searching range: 0.016748 to 0.0167482 Iteration 6, step size: 1.70109e-08, logL: -260643. Tao: 0.0167481, searching range: 0.0167481 to 0.0167481 Iteration 7, step size: 2.26811e-09, logL: -260643. Tao: 0.0167481, searching range: 0.0167481 to 0.0167481 Iter 4, tao: 0.0167481, Var(Y): 6.7279, fixed effects: 0.0028746 -0.00199494 -0.000117309 -0.000413687 0.000531721 0.0023796 -0.00231263 0.00347665 0.00057954 0.0108795 0.00507101 0.0382234 0.154268 -1.79709. fastGWA-BB-REML converged. fastGWA-BB-REML finished in 449.492 seconds. Tuning parameters using null SNPs... reading 200 SNP... 100% finished in 2.5 sec 200 SNPs have been processed. Not enough null SNPs. reading 200 SNP... 100% finished in 2.9 sec 200 SNPs have been processed. Mean GRAMMAR-Gamma value = 0.997378 Tuning time: 5.41415 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/CBP/CBP_self-rep_eur_exomes.fastGWA]. 1.7% Estimated time remaining 299.4 min 3.4% Estimated time remaining 296.5 min 5.0% Estimated time remaining 291.6 min 6.7% Estimated time remaining 287.3 min 8.4% Estimated time remaining 283.1 min 10.1% Estimated time remaining 277.5 min 11.8% Estimated time remaining 272.1 min 13.4% Estimated time remaining 267.4 min 15.1% Estimated time remaining 262.1 min 16.8% Estimated time remaining 256.8 min 18.4% Estimated time remaining 252.5 min 20.0% Estimated time remaining 248.0 min 21.7% Estimated time remaining 242.9 min 23.3% Estimated time remaining 237.8 min 24.9% Estimated time remaining 233.0 min 26.6% Estimated time remaining 227.7 min 28.3% Estimated time remaining 222.3 min 30.0% Estimated time remaining 217.1 min 31.7% Estimated time remaining 212.0 min 33.2% Estimated time remaining 207.2 min 34.9% Estimated time remaining 202.0 min 36.6% Estimated time remaining 196.7 min 38.3% Estimated time remaining 191.6 min 40.0% Estimated time remaining 186.4 min 41.6% Estimated time remaining 181.2 min 43.3% Estimated time remaining 176.0 min 45.0% Estimated time remaining 170.7 min 46.6% Estimated time remaining 165.9 min 48.3% Estimated time remaining 160.7 min 49.9% Estimated time remaining 155.8 min 51.5% Estimated time remaining 150.7 min 53.2% Estimated time remaining 145.5 min 54.8% Estimated time remaining 140.8 min 56.4% Estimated time remaining 136.0 min 58.1% Estimated time remaining 130.8 min 59.8% Estimated time remaining 125.5 min 61.4% Estimated time remaining 120.2 min 63.1% Estimated time remaining 114.9 min 64.8% Estimated time remaining 109.7 min 66.4% Estimated time remaining 104.8 min 68.0% Estimated time remaining 99.9 min 69.6% Estimated time remaining 94.7 min 71.2% Estimated time remaining 89.7 min 72.9% Estimated time remaining 84.5 min 74.6% Estimated time remaining 79.2 min 76.3% Estimated time remaining 74.0 min 78.0% Estimated time remaining 68.8 min 79.5% Estimated time remaining 64.2 min 80.9% Estimated time remaining 59.6 min 82.5% Estimated time remaining 54.7 min 84.2% Estimated time remaining 49.4 min 85.9% Estimated time remaining 44.1 min 87.6% Estimated time remaining 38.9 min 89.2% Estimated time remaining 33.9 min 90.7% Estimated time remaining 28.9 min 92.4% Estimated time remaining 23.7 min 94.0% Estimated time remaining 18.7 min 95.6% Estimated time remaining 13.8 min 97.2% Estimated time remaining 8.8 min 98.9% Estimated time remaining 3.5 min 100% finished in 18791.4 sec 17549650 SNPs have been processed. Saved 7890268 SNPs. Analysis finished at 18:54:10 +07 on Sat Nov 19 2022 Overall computational time: 5 hours 21 minutes 21 sec.