diff --git a/truvari/bench.py b/truvari/bench.py
index 9dc90d6..83aed73 100644
--- a/truvari/bench.py
+++ b/truvari/bench.py
@@ -145,7 +145,7 @@ def check_params(args):
         check_fail = True
     if args.reference:
         logging.warning("`--reference` is no longer recommended and will be deprecated by v5")
-        not os.path.exists(args.reference):
+        if not os.path.exists(args.reference):
             logging.error("Reference %s does not exist", args.reference)
         check_fail = True
     return check_fail
diff --git a/truvari/collapse.py b/truvari/collapse.py
index 4e56c8b..a138891 100644
--- a/truvari/collapse.py
+++ b/truvari/collapse.py
@@ -568,7 +568,7 @@ def check_params(args):
         logging.error("Using --hap must use --keep first")
     if args.reference:
         logging.warning("`--reference` is no longer recommended and will be deprecated by v5")
-        not os.path.exists(args.reference):
+        if not os.path.exists(args.reference):
             logging.error("Reference %s does not exist", args.reference)
         check_fail = True
     return check_fail