******************************************************************* * Genome-wide Complex Trait Analysis (GCTA) * version v1.95.1 Linux * Built at Feb 2 2026 16:51:42, by GCC 8.4 * (C) 2010-present, Yang Lab, Westlake University * Please report bugs to Jian Yang ******************************************************************* Analysis started at 05:44:51 MDT on Wed Jun 03 2026. Hostname: ip-10-0-200-228 Options: --fastGWA-mlm --bfile study2_qc --grm-sparse study2_sp_grm --pheno study2_pheno_gcta.txt --qcovar study2_covar_noPCs.txt --out study2_noPCs --thread-num 4 The program will be running with up to 4 threads. Reading PLINK FAM file from [study2_qc.fam]... 1971 individuals to be included from FAM file. Reading phenotype data from [study2_pheno_gcta.txt]... 1971 overlapping individuals with non-missing data to be included from the phenotype file. 1971 individuals to be included. 976 males, 995 females, 0 unknown. Reading PLINK BIM file from [study2_qc.bim]... 40479 SNPs to be included from BIM file(s). Reading quantitative covariates from [study2_covar_noPCs.txt]. 2 covariates of 2000 samples to be included. 1971 overlapping individuals with non-missing data to be included from the covariate file(s). Reading the sparse GRM file from [study2_sp_grm]... After matching all the files, 1971 individuals to be included in the analysis. Estimating the genetic variance (Vg) by fastGWA-REML (grid search)... Iteration 1, step size: 0.0172468, logL: -1027.5. Vg: 0.310443, searching range: 0.293196 to 0.32769 Iteration 2, step size: 0.00229958, logL: -1027.5. Vg: 0.316192, searching range: 0.313892 to 0.318491 Iteration 3, step size: 0.00030661, logL: -1027.5. Vg: 0.315732, searching range: 0.315425 to 0.316039 Iteration 4, step size: 4.08814e-05, logL: -1027.5. Vg: 0.315589, searching range: 0.315548 to 0.31563 Iteration 5, step size: 5.45085e-06, logL: -1027.5. Vg: 0.315581, searching range: 0.315575 to 0.315586 Iteration 6, step size: 7.2678e-07, logL: -1027.5. Vg: 0.315579, searching range: 0.315578 to 0.31558 Iteration 7, step size: 9.6904e-08, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 Iteration 8, step size: 1.29205e-08, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 Iteration 9, step size: 1.72274e-09, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 Iteration 10, step size: 2.29698e-10, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 Iteration 11, step size: 3.06264e-11, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 Iteration 12, step size: 4.08353e-12, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 Iteration 13, step size: 5.44472e-13, logL: -1027.5. Vg: 0.315579, searching range: 0.315579 to 0.315579 fastGWA-REML converged. logL: -1027.5 Sampling variance/covariance of the estimates of Vg and Ve: 0.0173252 -0.0166594 -0.0166594 0.0172193 Source Variance SE Vg 0.315579 0.131625 Ve 0.762348 0.131222 Vp 1.07793 Heritability = 0.292765 (Pval = 0.016505) fastGWA-REML runtime: 39.7095 sec. Tuning parameters using 2000 null SNPs... reading genotypes... 100% finished in 22.1 sec 1944 SNPs have been processed. Tuning of Gamma finished at the 1000th SNP. Mean GRAMMAR-Gamma value = 0.896260 Tuning of Gamma finished 22.0798 seconds. Performing fastGWA mixed model association analysis... fastGWA results will be saved in text format to [study2_noPCs.fastGWA]. Filtering out variants with MAF < 0.0001, or customise it with --maf flag. Filtering out variants with missingness rate > 0.10, or customise it with --geno flag. 100% finished in 0.2 sec 40479 SNPs have been processed. Saved 40479 SNPs. Analysis finished at 05:45:53 MDT on Wed Jun 03 2026 Overall computational time: 1 minute 2 sec.