*******************************************************************
* 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 14:39:22 UTC on Tue Mar 05 2019.
Hostname: workshop-11

Accepted options:
--grm mydata_allSNPs
--pheno mydata.phen
--mpheno 2
--reml
--keep unrelated.singleton.txt
--out trait2_allSNPs

Note: the program will be running on 4 threads.

Reading IDs of the GRM from [mydata_allSNPs.grm.id].
6000 IDs read from [mydata_allSNPs.grm.id].
Reading the GRM from [mydata_allSNPs.grm.bin].
GRM for 6000 individuals are included from [mydata_allSNPs.grm.bin].
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].

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 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.501648 0.507082
logL: -2266.63
Running AI-REML algorithm ...
Iter.	logL	V(G)	V(e)	
1	-2266.11	0.49555	0.51406	
2	-2265.88	0.48143	0.52999	
3	-2265.64	0.47955	0.53153	
4	-2265.64	0.47935	0.53168	
5	-2265.64	0.47933	0.53170	
Log-likelihood ratio converged.

Calculating the logLikelihood for the reduced model ...
(variance component 1 is dropped from the model)
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.99804
logL: -2403.01250
Running AI-REML algorithm ...
Iter.	logL	V(e)	
1	-2403.01	0.99804	
Log-likelihood ratio converged.

Summary result of REML analysis:
Source	Variance	SE
V(G)	0.479330	0.031773
V(e)	0.531696	0.024740
Vp	1.011026	0.022118
V(G)/Vp	0.474102	0.026153

Sampling variance/covariance of the estimates of variance components:
1.009536e-03	-5.662076e-04	
-5.662076e-04	6.120842e-04	

Summary result of REML analysis has been saved in the file [trait2_allSNPs.hsq].

Analysis finished at 14:42:37 UTC on Tue Mar 05 2019
Computational time: 3 minutes 15 second(s).