Small fixes in ukb_analysis

AlexTISYoung · Dec 3, 2024 · e1951da · e1951da
1 parent ed11c7f
commit e1951da
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Showing 2 changed files with 1 addition and 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
@@ -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
@@ -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