*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version v1.95.1 Linux
* Built at Feb  2 2026 16:51:42, by GCC 8.4
* (C) 2010-present, Yang Lab, Westlake University
* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 17:50:49 MDT on Mon Jun 01 2026.
Hostname: ip-10-0-202-51

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 16 threads.

Reading IDs of the GRM from [mydata_allSNPs.grm.id].
6000 IDs are 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 4804 individuals (1196 individuals removed).

4804 individuals are in common in these files.

Performing  REML analysis ... (Note: may take hours depending on sample size).
4804 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: 0.493555 0.542262
logL: -2395.04
Running AI-REML algorithm ...
Iter.	logL	V(G)	V(e)	
1	-2380.83	0.41602	0.59801	
2	-2362.10	0.36507	0.63895	
3	-2353.23	0.33121	0.66830	
4	-2349.07	0.30857	0.68898	
5	-2347.14	0.29337	0.70336	
6	-2346.24	0.28315	0.71329	
7	-2345.83	0.26135	0.73481	
8	-2345.48	0.26200	0.73454	
9	-2345.48	0.26199	0.73455	
10	-2345.48	0.26199	0.73455	
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: 0.99813
logL: -2401.25458
Running AI-REML algorithm ...
Iter.	logL	V(e)	
1	-2401.25	0.99813	
Log-likelihood ratio converged.

Summary result of REML analysis:
Source	Variance	SE
V(G)	0.261986	0.027990
V(e)	0.734552	0.027633
Vp	0.996538	0.020777
V(G)/Vp	0.262896	0.026446

Sampling variance/covariance of the estimates of variance components:
7.834348e-04	-5.576675e-04	
-5.576675e-04	7.635794e-04	

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

Analysis finished at 17:51:30 MDT on Mon Jun 01 2026
Overall computational time: 41.80 sec.