*******************************************************************
* 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 14:25:44 UTC on Tue Mar 05 2019.
Hostname: workshop-11

Accepted options:
--grm mydata_allSNPs
--pheno mydata.phen
--mpheno 1
--reml
--out trait1_with_relatives

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 #1 is included for analysis.
Non-missing phenotypes of 6000 individuals are included from [mydata.phen].

6000 individuals are in common in these files.

Performing  REML analysis ... (Note: may take hours depending on sample size).
6000 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: 0.486023 0.510111
logL: -2734.82
Running AI-REML algorithm ...
Iter.	logL	V(G)	V(e)	
1	-2730.12	0.45807	0.53045	
2	-2725.86	0.43914	0.54497	
3	-2723.83	0.42627	0.55520	
4	-2722.86	0.41750	0.56235	
5	-2722.41	0.39855	0.57805	
6	-2722.00	0.39855	0.57828	
7	-2722.00	0.39855	0.57828	
8	-2722.00	0.39855	0.57828	
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: 0.97663
logL: -2932.90880
Running AI-REML algorithm ...
Iter.	logL	V(e)	
1	-2932.91	0.97663	
Log-likelihood ratio converged.

Summary result of REML analysis:
Source	Variance	SE
V(G)	0.398550	0.023990
V(e)	0.578277	0.019175
Vp	0.976827	0.019107
V(G)/Vp	0.408004	0.020539

Sampling variance/covariance of the estimates of variance components:
5.755011e-04	-2.890503e-04	
-2.890503e-04	3.676819e-04	

Summary result of REML analysis has been saved in the file [trait1_with_relatives.hsq].

Analysis finished at 14:33:08 UTC on Tue Mar 05 2019
Computational time: 7 minutes 24 second(s).