******************************************************************* * 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 17:54:00 MDT on Mon Jun 01 2026. Hostname: ip-10-0-202-51 Accepted options: --grm mydata_allSNPs --pheno mydata.phen --mpheno 2 --reml --keep unrelated.singleton.txt --out trait2_allSNPs Note: the program will be running on 16 threads. Reading IDs of the GRM from [mydata_allSNPs.grm.id]. 6000 IDs are read from [mydata_allSNPs.grm.id]. Reading the GRM from [mydata_allSNPs.grm.bin]. GRM for 6000 individuals are included from [mydata_allSNPs.grm.bin]. Reading phenotypes from [mydata.phen]. There are 2 traits specified in the file [mydata.phen]. Trait #2 is included for analysis. Non-missing phenotypes of 6000 individuals are included from [mydata.phen]. 4804 individuals are kept from [unrelated.singleton.txt]. 4804 individuals are in common in these files. Performing REML analysis ... (Note: may take hours depending on sample size). 4804 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance). Calculating prior values of variance components by EM-REML ... Updated prior values: 0.503632 0.497865 logL: -2224.36 Running AI-REML algorithm ... Iter. logL V(G) V(e) 1 -2224.20 0.51653 0.48889 2 -2223.70 0.54574 0.46887 3 -2223.20 0.54839 0.46734 4 -2223.19 0.54859 0.46719 5 -2223.19 0.54861 0.46718 Log-likelihood ratio converged. Calculating the logLikelihood for the reduced model ... (variance component 1 is dropped from the model) Calculating prior values of variance components by EM-REML ... Updated prior values: 1.00041 logL: -2406.72472 Running AI-REML algorithm ... Iter. logL V(e) 1 -2406.72 1.00041 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G) 0.548611 0.031984 V(e) 0.467182 0.023087 Vp 1.015792 0.022572 V(G)/Vp 0.540082 0.024745 Sampling variance/covariance of the estimates of variance components: 1.022959e-03 -5.232479e-04 -5.232479e-04 5.330104e-04 Summary result of REML analysis has been saved in the file [trait2_allSNPs.hsq]. Analysis finished at 17:54:23 MDT on Mon Jun 01 2026 Overall computational time: 22.67 sec.