******************************************************************* * 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 00:18:06 UTC on Wed Jun 15 2022. Hostname: ip-10-0-201-15 Accepted options: --pheno ozht.phen --qcovar ozht.noprs.qcovar --covar ozht.covar --mgrm GRM-CRM.txt --out ozht.ACE.noPRS --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.noprs.qcovar]. 5 quantitative covariate(s) of 1933 individuals are included from [ozht.noprs.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]. 5 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, 7 fixed effect(s), and 3 variance component(s)(including residual variance). Calculating prior values of variance components by EM-REML ... Updated prior values: 29.9987 29.2238 24.6804 logL: -4743.2 Running AI-REML algorithm ... Iter. logL V(G1) V(G2) V(e) 1 -4707.94 50.50444 18.76735 13.48569 2 -4619.16 61.56774 14.52118 9.43760 3 -4580.06 68.11473 12.27247 7.82146 4 -4564.66 72.50874 10.89596 6.99949 5 -4557.87 75.58820 10.01934 6.52078 6 -4554.65 77.77308 9.45718 6.21996 7 -4553.08 79.32728 9.09780 6.02201 8 -4552.29 80.43283 8.86937 5.88786 9 -4551.89 82.92080 8.41252 5.59440 10 -4551.47 83.12611 8.49722 5.57181 11 -4551.46 83.17248 8.47906 5.56857 12 -4551.46 83.17167 8.48316 5.56815 Log-likelihood ratio converged. Summary result of REML analysis: Source Variance SE V(G1) 83.171674 5.244265 V(G2) 8.483162 3.649805 V(e) 5.568147 0.357947 Vp 97.222984 3.852488 V(G1)/Vp 0.855473 0.038053 V(G2)/Vp 0.087255 0.037572 Sum of V(G)/Vp 0.942728 0.004466 Sampling variance/covariance of the estimates of variance components: 2.750231e+01 -1.282423e+01 -2.550578e-01 -1.282423e+01 1.332108e+01 2.436311e-02 -2.550578e-01 2.436311e-02 1.281264e-01 Estimatesof fixed effects: Source Estimate SE mean 167.512988 8.941782 X_2 -0.111362 0.023243 X_3 0.698244 492.479954 X_4 381.639950 298.873360 X_5 44.964056 192.412455 X_6 -37.669274 182.522386 X_7 -9.586927 0.586907 Summary result of REML analysis has been saved in the file [ozht.ACE.noPRS.hsq]. Analysis finished at 00:18:09 UTC on Wed Jun 15 2022 Overall computational time: 3.34 sec.