*******************************************************************
* 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 14:33:08 UTC on Tue Mar 05 2019.
Hostname: workshop-11

Accepted options:
--grm mydata_allSNPs
--pheno mydata.phen
--mpheno 1
--reml
--out trait1_without_relatives
--grm-cutoff0.05

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].
Pruning the GRM with a cutoff of 0.05 ...
After pruning the GRM, there are 4808 individuals (1192 individuals removed).

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: 0.487519 0.535465
logL: -2370.42
Running AI-REML algorithm ...
Iter.	logL	V(G)	V(e)	
1	-2355.90	0.41109	0.59082	
2	-2337.22	0.36016	0.63191	
3	-2328.18	0.32588	0.66170	
4	-2323.86	0.30267	0.68291	
5	-2321.81	0.28689	0.69782	
6	-2320.84	0.27615	0.70822	
7	-2320.38	0.25297	0.73102	
8	-2319.98	0.25307	0.73126	
9	-2319.98	0.25307	0.73126	
10	-2319.98	0.25307	0.73126	
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: 0.98443
logL: -2370.01911
Running AI-REML algorithm ...
Iter.	logL	V(e)	
1	-2370.02	0.98443	
Log-likelihood ratio converged.

Summary result of REML analysis:
Source	Variance	SE
V(G)	0.253065	0.027906
V(e)	0.731259	0.027626
Vp	0.984324	0.020507
V(G)/Vp	0.257096	0.026772

Sampling variance/covariance of the estimates of variance components:
7.787418e-04	-5.607051e-04	
-5.607051e-04	7.631864e-04	

Summary result of REML analysis has been saved in the file [trait1_without_relatives.hsq].

Analysis finished at 14:39:22 UTC on Tue Mar 05 2019
Computational time: 6 minutes 13 second(s).