diff --git a/merge_wrapper.py b/merge_wrapper.py
index 4f850ae..14f2b7a 100755
--- a/merge_wrapper.py
+++ b/merge_wrapper.py
@@ -168,6 +168,8 @@ def fix_namedup(name):
 #if args.merging_length_cutoff:
 mergercall.append('-ml')
 mergercall.append(str(merging_length_cutoff))
+mergercall.append('-p')
+mergercall.append(str(prefix))
 
 #run the merging program
 if not args.stop_after_nucmer and not args.stop_after_df and not args.clean_only: