PLINK v2.00a2LM AVX2 Intel (12 Nov 2019) Options in effect: --bpfile /oak/stanford/groups/mrivas/private_data/ukbb/24983/cal/pgen/ukb24983_cal_cALL_v2_hg19 --chr 1-22 --covar /oak/stanford/groups/mrivas/ukbb24983/sqc/ukb24983_GWAS_covar.phe --covar-name age sex Array PC1-PC4 --exclude /oak/stanford/groups/mrivas/private_data/ukbb/24983/sqc/one_array_variants.txt --glm firth-fallback hide-covar omit-ref --keep /oak/stanford/groups/mrivas/ukbb24983/sqc/population_stratification/ukb24983_white_british.phe --memory 32000 --out /oak/stanford/groups/mrivas/projects/ANGPTL7/ukbb_gwas/white_british/ukb24983_v2_hg19.INI5262.genotyped.both_arrays --pheno /oak/stanford/groups/mrivas/ukbb24983/phenotypedata/extras/iop/phe/INI5262.phe --pheno-quantile-normalize --remove /oak/stanford/groups/mrivas/ukbb24983/sqc/ukb24983_v2.not_used_in_pca.phe --threads 4 Hostname: sh-109-55.int Working directory: /oak/stanford/groups/mrivas/users/ytanigaw/repos/rivas-lab/ANGPTL7/notebook/ukbb_gwas Start time: Wed Nov 20 13:56:16 2019 Random number seed: 1574286976 385192 MiB RAM detected; reserving 32000 MiB for main workspace. Using up to 4 compute threads. 488377 samples (264861 females, 223509 males, 7 ambiguous; 488377 founders) loaded from /oak/stanford/groups/mrivas/private_data/ukbb/24983/cal/pgen/ukb24983_cal_cALL_v2_hg19.fam. 784256 out of 805426 variants loaded from /oak/stanford/groups/mrivas/private_data/ukbb/24983/cal/pgen/ukb24983_cal_cALL_v2_hg19.bim. 1 quantitative phenotype loaded (123572 values). --exclude: 728270 variants remaining. --keep: 337151 samples remaining. --remove: 337151 samples remaining. 7 covariates loaded from /oak/stanford/groups/mrivas/ukbb24983/sqc/ukb24983_GWAS_covar.phe. 337151 samples (181034 females, 156117 males; 337151 founders) remaining after main filters. 81401 quantitative phenotype values remaining after main filters. --pheno-quantile-normalize: 1 phenotype transformed. 728270 variants remaining after main filters. --glm linear regression on phenotype 'INI5262': done. Results written to /oak/stanford/groups/mrivas/projects/ANGPTL7/ukbb_gwas/white_british/ukb24983_v2_hg19.INI5262.genotyped.both_arrays.INI5262.glm.linear . End time: Wed Nov 20 14:10:06 2019 PLINK v2.00a2LM AVX2 Intel (12 Nov 2019) Options in effect: --bpfile /oak/stanford/groups/mrivas/private_data/ukbb/24983/cal/pgen/ukb24983_cal_cALL_v2_hg19 --chr 1-22 --covar /oak/stanford/groups/mrivas/ukbb24983/sqc/ukb24983_GWAS_covar.phe --covar-name age sex PC1-PC4 --extract /oak/stanford/groups/mrivas/private_data/ukbb/24983/sqc/one_array_variants.txt --glm firth-fallback hide-covar omit-ref --keep /oak/stanford/groups/mrivas/ukbb24983/sqc/population_stratification/ukb24983_white_british.phe --memory 32000 --out /oak/stanford/groups/mrivas/projects/ANGPTL7/ukbb_gwas/white_british/ukb24983_v2_hg19.INI5262.genotyped.one_array --pheno /oak/stanford/groups/mrivas/ukbb24983/phenotypedata/extras/iop/phe/INI5262.phe --pheno-quantile-normalize --remove /oak/stanford/groups/mrivas/ukbb24983/sqc/ukb24983_v2.not_used_in_pca.phe --threads 4 Hostname: sh-109-55.int Working directory: /oak/stanford/groups/mrivas/users/ytanigaw/repos/rivas-lab/ANGPTL7/notebook/ukbb_gwas Start time: Wed Nov 20 13:55:36 2019 Random number seed: 1574286936 385192 MiB RAM detected; reserving 32000 MiB for main workspace. Using up to 4 compute threads. 488377 samples (264861 females, 223509 males, 7 ambiguous; 488377 founders) loaded from /oak/stanford/groups/mrivas/private_data/ukbb/24983/cal/pgen/ukb24983_cal_cALL_v2_hg19.fam. 784256 out of 805426 variants loaded from /oak/stanford/groups/mrivas/private_data/ukbb/24983/cal/pgen/ukb24983_cal_cALL_v2_hg19.bim. 1 quantitative phenotype loaded (123572 values). --extract: 55986 variants remaining. --keep: 337151 samples remaining. --remove: 337151 samples remaining. 6 covariates loaded from /oak/stanford/groups/mrivas/ukbb24983/sqc/ukb24983_GWAS_covar.phe. 337151 samples (181034 females, 156117 males; 337151 founders) remaining after main filters. 81401 quantitative phenotype values remaining after main filters. --pheno-quantile-normalize: 1 phenotype transformed. 55986 variants remaining after main filters. --glm linear regression on phenotype 'INI5262': done. Results written to /oak/stanford/groups/mrivas/projects/ANGPTL7/ukbb_gwas/white_british/ukb24983_v2_hg19.INI5262.genotyped.one_array.INI5262.glm.linear . End time: Wed Nov 20 13:56:15 2019