******************************************************************* * 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 17:54:23 MDT on Mon Jun 01 2026. Hostname: ip-10-0-202-51 Accepted options: --mgrm mgrm.txt --pheno mydata.phen --mpheno 2 --reml --keep unrelated.singleton.txt --out trait2_maf_stratified Note: the program will be running on 16 threads. 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]. There are 2 GRM file names specified in the file [mgrm.txt]. Reading the GRM from the 1th file ... Reading IDs of the GRM from [mydata_maf_below_0.05.grm.id]. 6000 IDs are read from [mydata_maf_below_0.05.grm.id]. Reading the GRM from [mydata_maf_below_0.05.grm.bin]. GRM for 6000 individuals are included from [mydata_maf_below_0.05.grm.bin]. Reading the GRM from the 2th file ... Reading IDs of the GRM from [mydata_maf_above_0.05.grm.id]. 6000 IDs are read from [mydata_maf_above_0.05.grm.id]. Reading the GRM from [mydata_maf_above_0.05.grm.bin]. GRM for 6000 individuals are included from [mydata_maf_above_0.05.grm.bin]. 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 3 variance component(s)(including residual variance). Calculating prior values of variance components by EM-REML ... Updated prior values: 0.354622 0.286229 0.299947 logL: -1367.11 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -1290.72 0.40974 0.14679 0.33739 2 -1165.23 0.45571 0.09452 0.35378 3 -1124.79 0.49338 0.06815 0.36240 4 -1108.11 0.52321 0.05310 0.36735 5 -1100.62 0.54610 0.04391 0.37037 6 -1097.13 0.56317 0.03806 0.37229 7 -1095.48 0.57564 0.03425 0.37354 8 -1094.70 0.58459 0.03171 0.37437 9 -1094.33 0.60466 0.02631 0.37614 10 -1094.00 0.60547 0.02635 0.37614 11 -1094.00 0.60548 0.02634 0.37614 12 -1094.00 0.60548 0.02634 0.37614 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 0.605476 0.034624 V(G2) 0.026344 0.011579 V(e) 0.376139 0.013897 Vp 1.007958 0.035287 V(G1)/Vp 0.600695 0.015007 V(G2)/Vp 0.026136 0.011510 Sum of V(G)/Vp 0.626831 0.017852 Sampling variance/covariance of the estimates of variance components: 1.198835e-03 -4.605844e-06 -1.283485e-05 -4.605844e-06 1.340827e-04 -1.230118e-04 -1.283485e-05 -1.230118e-04 1.931285e-04 Summary result of REML analysis has been saved in the file [trait2_maf_stratified.hsq]. Analysis finished at 17:55:13 MDT on Mon Jun 01 2026 Overall computational time: 49.53 sec.