diff --git a/truvari/bench.py b/truvari/bench.py
index 83aed73a..2b880852 100644
--- a/truvari/bench.py
+++ b/truvari/bench.py
@@ -147,7 +147,7 @@ def check_params(args):
         logging.warning("`--reference` is no longer recommended and will be deprecated by v5")
         if not os.path.exists(args.reference):
             logging.error("Reference %s does not exist", args.reference)
-        check_fail = True
+            check_fail = True
     return check_fail
 
 
diff --git a/truvari/collapse.py b/truvari/collapse.py
index a1388912..e715d924 100644
--- a/truvari/collapse.py
+++ b/truvari/collapse.py
@@ -570,7 +570,7 @@ def check_params(args):
         logging.warning("`--reference` is no longer recommended and will be deprecated by v5")
         if not os.path.exists(args.reference):
             logging.error("Reference %s does not exist", args.reference)
-        check_fail = True
+            check_fail = True
     return check_fail