******************************************************************* * Genome-wide Complex Trait Analysis (GCTA) * version v1.94.1 Linux * Built at Dec 16 2024 16:35:13, by GCC 8.3 * (C) 2010-present, Yang Lab, Westlake University * Please report bugs to Jian Yang ******************************************************************* Analysis started at 16:53:09 MST on Mon Mar 03 2025. Hostname: ip-10-0-201-101 Options: --bfile 1kg_hm3_qced --remove AMR.id --make-grm --out myGRM_noAMR The program will be running with up to 2 threads. Note: GRM is computed using the SNPs on the autosomes. Reading PLINK FAM file from [1kg_hm3_qced.fam]... 2504 individuals to be included from FAM file. Get 347 samples from list [AMR.id]. After removing individuals, 2157 subjects remain. 2157 individuals to be included. 0 males, 0 females, 2157 unknown. Reading PLINK BIM file from [1kg_hm3_qced.bim]... 80244 SNPs to be included from BIM file(s). Computing the genetic relationship matrix (GRM) v2 ... Subset 1/1, no. subject 1-2157 2157 samples, 80244 markers, 2327403 GRM elements IDs for the GRM file have been saved in the file [myGRM_noAMR.grm.id] Computing GRM... 100% finished in 4.9 sec 80244 SNPs have been processed. Used 80244 valid SNPs. The GRM computation is completed. Saving GRM... GRM has been saved in the file [myGRM_noAMR.grm.bin] Number of SNPs in each pair of individuals has been saved in the file [myGRM_noAMR.grm.N.bin] Analysis finished at 16:53:14 MST on Mon Mar 03 2025 Overall computational time: 5.20 sec.