******************************************************************* * 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 05:35:24 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_noPCs.txt --out study1_noPCs --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_noPCs.txt]. 2 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: 0.0163933, logL: -1004.93. Vg: 0.131146, searching range: 0.114753 to 0.14754 Iteration 2, step size: 0.00218577, logL: -1004.93. Vg: 0.134425, searching range: 0.132239 to 0.136611 Iteration 3, step size: 0.000291437, logL: -1004.93. Vg: 0.134279, searching range: 0.133988 to 0.134571 Iteration 4, step size: 3.88582e-05, logL: -1004.93. Vg: 0.134377, searching range: 0.134338 to 0.134415 Iteration 5, step size: 5.18109e-06, logL: -1004.93. Vg: 0.134374, searching range: 0.134369 to 0.134379 Iteration 6, step size: 6.90812e-07, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134377 Iteration 7, step size: 9.21083e-08, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 Iteration 8, step size: 1.22811e-08, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 Iteration 9, step size: 1.63748e-09, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 Iteration 10, step size: 1.09165e-10, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 Iteration 11, step size: 1.45554e-11, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 Iteration 12, step size: 1.94072e-12, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 Iteration 13, step size: 2.58763e-13, logL: -1004.93. Vg: 0.134376, searching range: 0.134376 to 0.134376 fastGWA-REML converged. logL: -1004.93 Sampling variance/covariance of the estimates of Vg and Ve: 0.00911951 -0.00889659 -0.00889659 0.00974833 Source Variance SE Vg 0.134376 0.0954961 Ve 0.890205 0.0987336 Vp 1.02458 Heritability = 0.131152 (Pval = 0.159386) fastGWA-REML runtime: 33.6155 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_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 40624 SNPs have been processed. Saved 40624 SNPs. Analysis finished at 05:35:59 MDT on Wed Jun 03 2026 Overall computational time: 34.15 sec.