diff --git a/run.sh b/run.sh
index bbc82094..f2f2ae7c 100755
--- a/run.sh
+++ b/run.sh
@@ -125,7 +125,7 @@ cmd="python $p.py \
 JOB_ID=$(submit "$cmd" $p)
 JOBS+=($JOB_ID)
 
-for s in "${SEQ_IDS[@]}"; do  # per chromosome
+for s in $(echo "$SEQ_IDS" | tr ',' ' '); do  # per chromosome
   p=clipped_read_distance
   cmd="python $p.py \
     -b \"$BAM\" \
@@ -161,7 +161,7 @@ done
 waiting
 
 # generate chromosome arrays from the channels as well as label window pairs
-for s in "${SEQ_IDS[@]}"; do
+for s in $(echo "$SEQ_IDS" | tr ',' ' '); do
   p=chr_array
   cmd="python $p.py \
     -b \"$BAM\" \