******************************************************************* * Genome-wide Complex Trait Analysis (GCTA) * version 1.94.0 beta Linux * (C) 2010-present, Jian Yang, The University of Queensland * Please report bugs to Jian Yang ******************************************************************* Analysis started at 00:17:51 UTC on Wed Jun 15 2022. Hostname: ip-10-0-201-15 Accepted options: --pheno ozht.phen --qcovar ozht.prs2.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS2.ACE --reml --reml-est-fix Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine. Reading phenotypes from [ozht.phen]. Non-missing phenotypes of 1895 individuals are included from [ozht.phen]. Reading quantitative covariate(s) from [ozht.prs2.qcovar]. 6 quantitative covariate(s) of 1933 individuals are included from [ozht.prs2.qcovar]. Reading discrete covariate(s) from [ozht.covar]. 1 discrete covariate(s) of 1933 individuals are included from [ozht.covar]. There are 2 GRM file names specified in the file [GRM-CRM.txt]. Reading the GRM from the 1th file ... Reading IDs of the GRM from [ozGRM.grm.id]. 1956 IDs are read from [ozGRM.grm.id]. Reading the GRM from [ozGRM.grm.bin]. GRM for 1956 individuals are included from [ozGRM.grm.bin]. Reading the GRM from the 2th file ... Reading IDs of the GRM from [ozCRM.grm.id]. 1956 IDs are read from [ozCRM.grm.id]. Reading the GRM from [ozCRM.grm.bin]. GRM for 1956 individuals are included from [ozCRM.grm.bin]. 6 quantitative variable(s) included as covariate(s). 1 discrete variable(s) included as covariate(s). 1894 individuals are in common in these files. Performing REML analysis ... (Note: may take hours depending on sample size). 1894 observations, 8 fixed effect(s), and 3 variance component(s)(including residual variance). Calculating prior values of variance components by EM-REML ... Updated prior values: 29.8995 29.0562 24.6377 logL: -4733.47 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -4697.25 50.24276 18.04696 13.61573 2 -4609.52 61.21929 13.64557 9.56059 3 -4570.92 67.72897 11.33108 7.91190 4 -4555.47 72.08346 9.92817 7.06959 5 -4548.62 75.12825 9.04166 6.57814 6 -4545.42 77.28681 8.47638 6.26889 7 -4543.77 78.82292 8.11645 6.06511 8 -4542.96 79.91706 7.88831 5.92680 9 -4542.55 82.38431 7.43282 5.62374 10 -4542.11 82.60353 7.51772 5.59911 11 -4542.11 82.65447 7.49848 5.59543 12 -4542.11 82.65387 7.50293 5.59492 13 -4542.11 82.65550 7.50186 5.59486 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 82.655495 5.190102 V(G2) 7.501856 3.565254 V(e) 5.594857 0.360340 Vp 95.752208 3.801264 V(G1)/Vp 0.863223 0.037804 V(G2)/Vp 0.078347 0.037294 Sum of V(G)/Vp 0.941569 0.004571 Sampling variance/covariance of the estimates of variance components: 2.693716e+01 -1.242863e+01 -2.588074e-01 -1.242863e+01 1.271104e+01 2.321948e-02 -2.588074e-01 2.321948e-02 1.298450e-01 Estimatesof fixed effects: Source Estimate SE mean 168.624485 8.862613 X_2 -0.110984 0.022994 X_3 -17.724625 488.242119 X_4 409.842479 296.195655 X_5 43.235878 190.742260 X_6 -55.042364 180.962099 X_7 3.174626 0.717059 X_8 -9.508999 0.580801 Summary result of REML analysis has been saved in the file [ozhtPRS2.ACE.hsq]. Analysis finished at 00:17:55 UTC on Wed Jun 15 2022 Overall computational time: 3.91 sec.