******************************************************************* * 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 00:17:48 UTC on Wed Jun 15 2022. Hostname: ip-10-0-201-15 Accepted options: --pheno ozht.phen --qcovar ozht.prs1.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozhtPRS1.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.prs1.qcovar]. 6 quantitative covariate(s) of 1933 individuals are included from [ozht.prs1.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: 29.9405 29.1033 24.645 logL: -4736.31 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -4700.32 50.36555 18.19224 13.55946 2 -4611.85 61.35311 13.83297 9.51921 3 -4573.17 67.87119 11.53647 7.88367 4 -4557.75 72.23652 10.14153 7.04864 5 -4550.93 75.29060 9.25897 6.56151 6 -4547.69 77.45579 8.69594 6.25505 7 -4546.10 78.99608 8.33749 6.05316 8 -4545.30 80.09254 8.11040 5.91617 9 -4544.89 82.56309 7.65749 5.61614 10 -4544.46 82.77717 7.74327 5.59209 11 -4544.46 82.82704 7.72411 5.58854 12 -4544.46 82.82629 7.72855 5.58805 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 82.826286 5.203826 V(G2) 7.728551 3.584645 V(e) 5.588054 0.359747 Vp 96.142891 3.815144 V(G1)/Vp 0.861492 0.037840 V(G2)/Vp 0.080386 0.037338 Sum of V(G)/Vp 0.941878 0.004543 Sampling variance/covariance of the estimates of variance components: 2.707981e+01 -1.251748e+01 -2.574890e-01 -1.251748e+01 1.284968e+01 2.317447e-02 -2.574890e-01 2.317447e-02 1.294179e-01 Estimatesof fixed effects: Source Estimate SE mean 169.255966 8.892221 X_2 -0.112214 0.023057 X_3 -49.312966 489.526725 X_4 414.675174 296.962542 X_5 39.556627 191.180832 X_6 -31.085455 181.347441 X_7 3.071223 0.804539 X_8 -9.529359 0.582336 Summary result of REML analysis has been saved in the file [ozhtPRS1.ACE.hsq]. Analysis finished at 00:17:51 UTC on Wed Jun 15 2022 Overall computational time: 3.32 sec.