******************************************************************* * 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 16:53:57 MST on Mon Mar 03 2025. Hostname: ip-10-0-201-101 Accepted options: --bfile 1kg_hm3_qced --remove AMR.id --pc-loading myPCA_noAMR --out myPCA_noAMR_snp_loading Note: the program will be running on 2 threads. Reading PLINK FAM file from [1kg_hm3_qced.fam]. 2504 individuals to be included from [1kg_hm3_qced.fam]. 347 individuals are removed from [AMR.id] and there are 2157 individuals remaining. Reading PLINK BIM file from [1kg_hm3_qced.bim]. 80244 SNPs to be included from [1kg_hm3_qced.bim]. Reading PLINK BED file from [1kg_hm3_qced.bed] in SNP-major format ... Genotype data for 2157 individuals and 80244 SNPs to be included from [1kg_hm3_qced.bed]. Reading eigenvectors from [myPCA_noAMR.eigenvec]. 2 eigenvectors of 2157 individuals are included from [myPCA_noAMR.eigenvec]. Reading eigenvalues from [myPCA_noAMR.eigenval]. 2 eigenvalues are read from [myPCA_noAMR.eigenval] 2157 individuals in common between the input files are included in the analysis. Calculating allele frequencies ... Calculating PC loadings of SNPs... Saving the PC loadings of 80244 SNPs to [myPCA_noAMR_snp_loading.pcl] ... Analysis finished at 16:54:00 MST on Mon Mar 03 2025 Overall computational time: 2.63 sec.