******************************************************************* * 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 18:48:12 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/MCGMS_AYT_KIBAHA_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]. 108 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 108 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 87721 SNPs (78095 SNPs with MAF < 0.05). Reading phenotypes from [/home/mw489/Somo/blups.txt]. Non-missing phenotypes of 108 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]. 108 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). 108 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: 0.0101975 0.0100026 logL: 159.375 Running AI-REML algorithm ... Iter. logL V(G) V(e) 1 159.45 0.01026 0.00979 2 159.47 0.01036 0.00938 3 159.48 0.01027 0.00944 4 159.48 0.01029 0.00943 5 159.48 0.01029 0.00943 6 159.48 0.01029 0.00943 7 159.48 0.01029 0.00943 Log-likelihood ratio converged. Running association tests for 87721 SNPs ... Saving the results of the mixed linear model association analyses of 87721 SNPs to [/home/mw489/Somo/MCGMS_AYT_KIBAHA_TARI_81318.mlma] ... Analysis finished: Mon Aug 13 18:48:15 2018 Computational time: 0:0:3