******************************************************************* * 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 05:36:22 MDT on Wed Jun 03 2026. Hostname: ip-10-0-200-228 Options: --fastGWA-mlm --bfile study1_qc --grm-sparse study1_sp_grm --pheno study1_pheno_gcta.txt --qcovar study1_covar_withPCs.txt --out study1_withPCs --thread-num 4 The program will be running with up to 4 threads. Reading PLINK FAM file from [study1_qc.fam]... 1973 individuals to be included from FAM file. Reading phenotype data from [study1_pheno_gcta.txt]... 1973 overlapping individuals with non-missing data to be included from the phenotype file. 1973 individuals to be included. 994 males, 979 females, 0 unknown. Reading PLINK BIM file from [study1_qc.bim]... 40624 SNPs to be included from BIM file(s). Reading quantitative covariates from [study1_covar_withPCs.txt]. 12 covariates of 2000 samples to be included. 1973 overlapping individuals with non-missing data to be included from the covariate file(s). Reading the sparse GRM file from [study1_sp_grm]... After matching all the files, 1973 individuals to be included in the analysis. Estimating the genetic variance (Vg) by fastGWA-REML (grid search)... Iteration 1, step size: 0.0161088, logL: -996.474. Vg: 0, searching range: 0 to 0.0161088 Iteration 2, step size: 0.00107392, logL: -996.474. Vg: 0, searching range: 0 to 0.00107392 Iteration 3, step size: 7.15946e-05, logL: -996.474. Vg: 0, searching range: 0 to 7.15946e-05 Iteration 4, step size: 4.77297e-06, logL: -996.474. Vg: 0, searching range: 0 to 4.77297e-06 Iteration 5, step size: 3.18198e-07, logL: -996.474. Vg: 0, searching range: 0 to 3.18198e-07 Iteration 6, step size: 2.12132e-08, logL: -996.474. Vg: 0, searching range: 0 to 2.12132e-08 Iteration 7, step size: 1.41421e-09, logL: -996.474. Vg: 0, searching range: 0 to 1.41421e-09 Iteration 8, step size: 9.42809e-11, logL: -996.474. Vg: 0, searching range: 0 to 9.42809e-11 Iteration 9, step size: 6.28539e-12, logL: -996.474. Vg: 0, searching range: 0 to 6.28539e-12 Iteration 10, step size: 4.19026e-13, logL: -996.474. Vg: 0, searching range: 0 to 4.19026e-13 Iteration 11, step size: 2.79351e-14, logL: -996.474. Vg: 0, searching range: 0 to 2.79351e-14 Iteration 12, step size: 1.86234e-15, logL: -996.474. Vg: 0, searching range: 0 to 1.86234e-15 Iteration 13, step size: 1.24156e-16, logL: -996.474. Vg: 6.2078e-16, searching range: 4.96624e-16 to 7.44936e-16 fastGWA-REML converged. logL: -996.474 Sampling variance/covariance of the estimates of Vg and Ve: 0.0294457 -0.028973 -0.028973 0.029536 Source Variance SE Vg 6.2078e-16 0.171597 Ve 1.0068 0.171861 Vp 1.0068 Heritability = 6.16588e-16 (Pval = 1) fastGWA-REML runtime: 33.7993 sec. Warning: the estimate of Vg is not statistically significant (i.e., p > 0.05). This is likely because the number of closely related individuals in the sample is not large enough. In this case, the program will use linear regression for association test. Performing fastGWA linear regression analysis... fastGWA results will be saved in text format to [study1_withPCs.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 40624 SNPs have been processed. Saved 40624 SNPs. Analysis finished at 05:36:56 MDT on Wed Jun 03 2026 Overall computational time: 34.33 sec.