diff --git a/bin/average_nucleotide_identity.py b/bin/average_nucleotide_identity.py
index b53d9b6a..f033f5fc 100755
--- a/bin/average_nucleotide_identity.py
+++ b/bin/average_nucleotide_identity.py
@@ -904,6 +904,11 @@ def subsample_input(infiles):
             logger.error("This will cause issues with MUMmer and BLAST")
             logger.error("(exiting)")
             sys.exit(1)
+        if any(['(' in fname, ')' in fname]):
+            logger.error("File or directory '%s' contains parentheses", fname)
+            logger.error("This will cause issues with MUMmer and BLAST")
+            logger.error("(exiting)")
+            sys.exit(1)
 
     if args.labels and not os.path.isfile(args.labels):
         logger.error("Missing labels file: %s", args.labels)