*******************************************************************
* 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 <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 16:55:02 MST on Mon Mar 03 2025.
Hostname: ip-10-0-201-101

Accepted options:
--bfile 1kg_hm3_qced
--keep AMR.id
--project-loading myPCA_noAMR_snp_loading 2
--out AMR_PCA

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 kept from [AMR.id].
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 347 individuals and 80244 SNPs to be included from [1kg_hm3_qced.bed].
Reading PC loadings of SNPs from [myPCA_noAMR_snp_loading.pcl].
Number of PC loading vectors: 2
Number of SNPs in loading array: 80244.
Matching alleles...
Adjusting A1
 80244 SNPs are included for loading
Standardizing genotypes and projecting PCs...
Total number of subjects: 347

Processing subject number: 
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Finished, and the PCs have all been saved to AMR_PCA.proj.eigenvec

Analysis finished at 16:55:03 MST on Mon Mar 03 2025
Overall computational time: 1.29 sec.