******************************************************************* * Genome-wide Complex Trait Analysis (GCTA) * version 1.92.0 beta2 * (C) 2010-2018, The University of Queensland * Please report bugs to: Jian Yang ******************************************************************* Analysis started at 14:14:49 UTC on Tue Mar 05 2019. Hostname: workshop-11 Accepted options: --bfile mydata --max-maf 0.05 --make-grm-bin --out mydata_maf_below_0.05 Note: the program will be running on 4 threads. Reading PLINK FAM file from [mydata.fam]. 6000 individuals to be included from [mydata.fam]. Reading PLINK BIM file from [mydata.bim]. 12000 SNPs to be included from [mydata.bim]. Reading PLINK BED file from [mydata.bed] in SNP-major format ... Genotype data for 6000 individuals and 12000 SNPs to be included from [mydata.bed]. Calculating allele frequencies ... Filtering SNPs with MAF < 0.05 ... After filtering SNPs with MAF < 0.05, there are 797 SNPs (11203 SNPs with MAF > 0.05). Recoding genotypes (individual major mode) ... Calculating the genetic relationship matrix (GRM) ... (Note: default speed-optimized mode, may use huge RAM) Summary of the GRM: Mean of diagonals = 0.999928 Variance of diagonals = 0.0295261 Mean of off-diagonals = -0.000166684 Variance of off-diagonals = 0.00140535 GRM of 6000 individuals has been saved in the file [mydata_maf_below_0.05.grm.bin] (in binary format). Number of SNPs to calcuate the genetic relationship between each pair of individuals has been saved in the file [mydata_maf_below_0.05.grm.N.bin] (in binary format). IDs for the GRM file [mydata_maf_below_0.05.grm.bin] have been saved in the file [mydata_maf_below_0.05.grm.id]. Analysis finished at 14:15:00 UTC on Tue Mar 05 2019 Computational time: 11.288629 second(s).