*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.92.0 beta2
* (C) 2010-2018, The University of Queensland
* Please report bugs to: Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started at 14:42:37 UTC on Tue Mar 05 2019.
Hostname: workshop-11

Accepted options:
--mgrm mgrm.txt
--pheno mydata.phen
--mpheno 2
--reml
--keep unrelated.singleton.txt
--out trait2_maf_stratified

Note: the program will be running on 4 threads.

Reading phenotypes from [mydata.phen].
There are 2 traits specified in the file [mydata.phen].
Trait #2 is included for analysis.
Non-missing phenotypes of 6000 individuals are included from [mydata.phen].
4808 individuals are kept from [unrelated.singleton.txt].

There are 2 GRM file names specified in the file [mgrm.txt].
Reading the GRM from the 1th file ...
Reading IDs of the GRM from [mydata_maf_below_0.05.grm.id].
6000 IDs read from [mydata_maf_below_0.05.grm.id].
Reading the GRM from [mydata_maf_below_0.05.grm.bin].
GRM for 6000 individuals are included from [mydata_maf_below_0.05.grm.bin].
Reading the GRM from the 2th file ...
Reading IDs of the GRM from [mydata_maf_above_0.05.grm.id].
6000 IDs read from [mydata_maf_above_0.05.grm.id].
Reading the GRM from [mydata_maf_above_0.05.grm.bin].
GRM for 6000 individuals are included from [mydata_maf_above_0.05.grm.bin].
4808 individuals are in common in these files.

Performing  REML analysis ... (Note: may take hours depending on sample size).
4808 observations, 1 fixed effect(s), and 3 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.356346 0.283102 0.299952
logL: -1366.23
Running AI-REML algorithm ...
Iter.	logL	V(G1)	V(G2)	V(e)	
1	-1282.92	0.41333	0.12597	0.34394	
2	-1130.40	0.46110	0.07299	0.36206	
3	-1085.73	0.50048	0.04714	0.37138	
4	-1067.80	0.53181	0.03266	0.37665	
5	-1059.87	0.55588	0.02395	0.37980	
6	-1056.21	0.57386	0.01847	0.38177	
7	-1054.50	0.58697	0.01493	0.38302	
8	-1053.70	0.59636	0.01261	0.38384	
9	-1053.32	0.61737	0.00770	0.38554	
10	-1052.98	0.61805	0.00784	0.38546	
11	-1052.98	0.61805	0.00784	0.38546	
12	-1052.98	0.61805	0.00784	0.38546	
Log-likelihood ratio converged.

Summary result of REML analysis:
Source	Variance	SE
V(G1)	0.618051	0.035290
V(G2)	0.007838	0.011030
V(e)	0.385462	0.013896
Vp	1.011350	0.035904
V(G1)/Vp	0.611114	0.014835
V(G2)/Vp	0.007750	0.010906

Sum of V(G)/Vp	0.618864	0.018175

Sampling variance/covariance of the estimates of variance components:
1.245349e-03	1.832266e-06	-1.855143e-05	
1.832266e-06	1.216529e-04	-1.187967e-04	
-1.855143e-05	-1.187967e-04	1.931033e-04	

Summary result of REML analysis has been saved in the file [trait2_maf_stratified.hsq].

Analysis finished at 14:46:46 UTC on Tue Mar 05 2019
Computational time: 4 minutes 8 second(s).