*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.25.2
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Mon Aug 13 18:47:42 2018

Options:
--mlma 
--bfile /home/mw489/Somo/AllChrom_TZ
--keep /home/mw489/Somo/keeplist.txt
--maf 0.05
--pheno /home/mw489/Somo/blups.txt
--grm-bin /home/mw489/Somo/Kinship_TZ
--out /home/mw489/Somo/MCMDS_PYT_UKIRIGURU_TARI_81318
--thread-num 72

Note: the program will be running on 72 threads.

Reading PLINK FAM file from [/home/mw489/Somo/AllChrom_TZ.fam].
1344 individuals to be included from [/home/mw489/Somo/AllChrom_TZ.fam].
86 individuals are kept from [/home/mw489/Somo/keeplist.txt].
Reading PLINK BIM file from [/home/mw489/Somo/AllChrom_TZ.bim].
165816 SNPs to be included from [/home/mw489/Somo/AllChrom_TZ.bim].
Reading PLINK BED file from [/home/mw489/Somo/AllChrom_TZ.bed] in SNP-major format ...
Genotype data for 86 individuals and 165816 SNPs to be included from [/home/mw489/Somo/AllChrom_TZ.bed].
Calculating allele frequencies ...
Filtering SNPs with MAF > 0.05 ...
After filtering SNPs with MAF > 0.05, there are 82515 SNPs (83301 SNPs with MAF < 0.05).
Reading phenotypes from [/home/mw489/Somo/blups.txt].
Non-missing phenotypes of 86 individuals are included from [/home/mw489/Somo/blups.txt].
Reading IDs of the GRM from [/home/mw489/Somo/Kinship_TZ.grm.id].
1344 IDs read from [/home/mw489/Somo/Kinship_TZ.grm.id].
Reading the GRM from [/home/mw489/Somo/Kinship_TZ.grm.bin].
Pairwise genetic relationships between 1344 individuals are included from [/home/mw489/Somo/Kinship_TZ.grm.bin].
86 individuals are in common in these files.

Performing MLM association analyses (including the candidate SNP) ...

Performing  REML analysis ... (Note: may take hours depending on sample size).
86 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: 0.0246593 0.0190018
logL: 96.6028
Running AI-REML algorithm ...
Iter.	logL	V(G)	V(e)	
1	98.26	0.04067	0.00000	(1 component(s) constrained)
2	109.22	0.04519	0.00000	(1 component(s) constrained)
3	109.08	0.04918	0.00000	(1 component(s) constrained)
4	108.66	0.05979	0.00000	(1 component(s) constrained)
5	106.72	0.06258	0.00000	(1 component(s) constrained)
6	106.10	0.06271	0.00000	(1 component(s) constrained)
7	106.07	0.06271	0.00000	(1 component(s) constrained)
8	106.07	0.06271	0.00000	(1 component(s) constrained)
Log-likelihood ratio converged.

Running association tests for 82515 SNPs ...

Saving the results of the mixed linear model association analyses of 82515 SNPs to [/home/mw489/Somo/MCMDS_PYT_UKIRIGURU_TARI_81318.mlma] ...

Analysis finished: Mon Aug 13 18:47:45 2018
Computational time: 0:0:3