******************************************************************* * 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 00:18:02 UTC on Wed Jun 15 2022. Hostname: ip-10-0-201-15 Accepted options: --pheno ozht.phen --qcovar ozht.prs5.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS5.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.prs5.qcovar]. 6 quantitative covariate(s) of 1933 individuals are included from [ozht.prs5.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: 29.8578 29.0401 24.6464 logL: -4732.1 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -4695.94 49.99573 18.17732 13.71870 2 -4609.97 60.96663 13.80366 9.62128 3 -4571.39 67.46612 11.51264 7.94896 4 -4555.83 71.80684 10.12860 7.09504 5 -4548.92 74.84089 9.25582 6.59709 6 -4545.64 76.99269 8.70006 6.28385 7 -4544.02 78.52530 8.34655 6.07745 8 -4543.20 79.61813 8.12264 5.93734 9 -4542.78 82.08548 7.67591 5.63026 10 -4542.34 82.31263 7.75955 5.60502 11 -4542.33 82.36451 7.74045 5.60120 12 -4542.33 82.36411 7.74491 5.60067 13 -4542.33 82.36578 7.74383 5.60060 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 82.365776 5.177148 V(G2) 7.743826 3.562831 V(e) 5.600599 0.360904 Vp 95.710201 3.800263 V(G1)/Vp 0.860575 0.037789 V(G2)/Vp 0.080909 0.037278 Sum of V(G)/Vp 0.941484 0.004581 Sampling variance/covariance of the estimates of variance components: 2.680287e+01 -1.235535e+01 -2.610650e-01 -1.235535e+01 1.269376e+01 2.397526e-02 -2.610650e-01 2.397526e-02 1.302519e-01 Estimatesof fixed effects: Source Estimate SE mean 168.700024 8.866271 X_2 -0.111501 0.023010 X_3 -48.135786 488.464289 X_4 416.564314 296.337132 X_5 36.881111 190.792892 X_6 -48.392397 180.984907 X_7 2.694306 0.611060 X_8 -9.536273 0.581096 Summary result of REML analysis has been saved in the file [ozhtPRS5.ACE.hsq]. Analysis finished at 00:18:06 UTC on Wed Jun 15 2022 Overall computational time: 3.69 sec.