******************************************************************* * 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 00:17:55 UTC on Wed Jun 15 2022. Hostname: ip-10-0-201-15 Accepted options: --pheno ozht.phen --qcovar ozht.prs3.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS3.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.prs3.qcovar]. 6 quantitative covariate(s) of 1933 individuals are included from [ozht.prs3.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: 29.8736 29.0475 24.6513 logL: -4732.9 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -4696.82 50.02688 18.17504 13.71829 2 -4610.66 61.02046 13.79117 9.62093 3 -4572.02 67.54188 11.49160 7.94854 4 -4556.43 71.90039 10.10100 7.09463 5 -4549.51 74.94802 9.22342 6.59669 6 -4546.22 77.10985 8.66428 6.28347 7 -4544.60 78.64964 8.30847 6.07709 8 -4543.78 79.74753 8.08303 5.93699 9 -4543.36 82.22597 7.63312 5.62996 10 -4542.92 82.45294 7.71726 5.60473 11 -4542.91 82.50486 7.69811 5.60091 12 -4542.91 82.50445 7.70257 5.60038 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 82.504446 5.185024 V(G2) 7.702573 3.566877 V(e) 5.600383 0.360921 Vp 95.807403 3.803911 V(G1)/Vp 0.861149 0.037795 V(G2)/Vp 0.080396 0.037284 Sum of V(G)/Vp 0.941545 0.004576 Sampling variance/covariance of the estimates of variance components: 2.688447e+01 -1.239669e+01 -2.609154e-01 -1.239669e+01 1.272261e+01 2.379670e-02 -2.609154e-01 2.379670e-02 1.302641e-01 Estimatesof fixed effects: Source Estimate SE mean 168.920692 8.871584 X_2 -0.110747 0.023017 X_3 -52.781755 488.696356 X_4 419.085643 296.469356 X_5 36.336875 190.868926 X_6 -44.344298 181.043903 X_7 2.813868 0.661025 X_8 -9.527183 0.581309 Summary result of REML analysis has been saved in the file [ozhtPRS3.ACE.hsq]. Analysis finished at 00:17:59 UTC on Wed Jun 15 2022 Overall computational time: 3.37 sec.