From e1951daf66b54822b10791e6854425b34aa9b664 Mon Sep 17 00:00:00 2001 From: Junming Guan Date: Tue, 3 Dec 2024 15:10:16 -0500 Subject: [PATCH] Small fixes in ukb_analysis --- paper_results/ukb_analysis/all_ancestries/robust/run_fgwas.sh | 3 +-- .../ukb_analysis/european/unified/run_fgwas_no_sex_covar.sh | 1 - 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/paper_results/ukb_analysis/all_ancestries/robust/run_fgwas.sh b/paper_results/ukb_analysis/all_ancestries/robust/run_fgwas.sh index 3a8706b8..5a03fc62 100644 --- a/paper_results/ukb_analysis/all_ancestries/robust/run_fgwas.sh +++ b/paper_results/ukb_analysis/all_ancestries/robust/run_fgwas.sh @@ -1,10 +1,9 @@ source ${snipar_env}/bin/activate set -e -outdir=/disk/genetics/ukb/jguan/ukb_analysis/output/gwas/new_robust/with_grm for i in {1..10} {14..18}; do - name=$(head -n 1 /disk/genetics/ukb/jguan/ukb_analysis/output/processed_traits_noadj_allancestry.txt | awk -v var=$i '{ print $((2+var)) }') + name=$(head -n 1 ${PHEN_PATH}/processed_traits_noadj_allancestry.txt | awk -v var=$i '{ print $((2+var)) }') echo $name $i if [ ! -d "$outdir/$name" ] then diff --git a/paper_results/ukb_analysis/european/unified/run_fgwas_no_sex_covar.sh b/paper_results/ukb_analysis/european/unified/run_fgwas_no_sex_covar.sh index ff4f7072..5e54f142 100644 --- a/paper_results/ukb_analysis/european/unified/run_fgwas_no_sex_covar.sh +++ b/paper_results/ukb_analysis/european/unified/run_fgwas_no_sex_covar.sh @@ -6,7 +6,6 @@ set -e for i in 11 12 13 18; do name=$(head -n 1 ${PHEN_PATH}/processed_traits_noadj.txt | awk -v var=$i '{ print $((2+var)) }') - echo $name $i if [ ! -d "$outdir/$name" ] then mkdir $outdir/$name