******************************************************************* * 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 00:17:59 UTC on Wed Jun 15 2022. Hostname: ip-10-0-201-15 Accepted options: --pheno ozht.phen --qcovar ozht.prs4.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS4.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.prs4.qcovar]. 6 quantitative covariate(s) of 1933 individuals are included from [ozht.prs4.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: 29.8714 29.0453 24.6475 logL: -4732.7 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -4696.57 50.05982 18.14688 13.69875 2 -4610.19 61.03608 13.76834 9.61007 3 -4571.60 67.54205 11.47352 7.94229 4 -4556.05 71.88905 10.08655 7.09055 5 -4549.15 74.92784 9.21178 6.59380 6 -4545.87 77.08286 8.65476 6.28129 7 -4544.25 78.61747 8.30052 6.07537 8 -4543.44 79.71148 8.07621 5.93558 9 -4543.02 82.18079 7.62885 5.62923 10 -4542.58 82.40633 7.71308 5.60410 11 -4542.57 82.45812 7.69390 5.60030 12 -4542.57 82.45766 7.69839 5.59977 13 -4542.57 82.45932 7.69729 5.59971 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 82.459325 5.181032 V(G2) 7.697294 3.563947 V(e) 5.599706 0.360812 Vp 95.756325 3.801953 V(G1)/Vp 0.861137 0.037783 V(G2)/Vp 0.080384 0.037273 Sum of V(G)/Vp 0.941521 0.004577 Sampling variance/covariance of the estimates of variance components: 2.684309e+01 -1.237322e+01 -2.605583e-01 -1.237322e+01 1.270172e+01 2.370034e-02 -2.605583e-01 2.370034e-02 1.301853e-01 Estimatesof fixed effects: Source Estimate SE mean 168.476664 8.865994 X_2 -0.110867 0.023012 X_3 -35.580670 488.477468 X_4 415.705483 296.370772 X_5 36.669483 190.821852 X_6 -47.537680 181.007689 X_7 2.723517 0.626279 X_8 -9.520307 0.581206 Summary result of REML analysis has been saved in the file [ozhtPRS4.ACE.hsq]. Analysis finished at 00:18:02 UTC on Wed Jun 15 2022 Overall computational time: 3.72 sec.