diff --git a/CHEWBBACA/__init__.py b/CHEWBBACA/__init__.py
index 39ebcde3..e665f756 100644
--- a/CHEWBBACA/__init__.py
+++ b/CHEWBBACA/__init__.py
@@ -1,2 +1,2 @@
 
-__version__ = "3.3.3"
+__version__ = "3.3.4"
diff --git a/CHEWBBACA/docs/conf.py b/CHEWBBACA/docs/conf.py
index f8a2f460..e0e9cded 100644
--- a/CHEWBBACA/docs/conf.py
+++ b/CHEWBBACA/docs/conf.py
@@ -22,7 +22,7 @@
 author = 'Rafael Mamede'
 
 # The full version, including alpha/beta/rc tags
-release = '3.3.3'
+release = '3.3.4'
 
 # -- General configuration ---------------------------------------------------
 
diff --git a/CHEWBBACA/utils/parameters_validation.py b/CHEWBBACA/utils/parameters_validation.py
index 86bae81f..bf569f12 100644
--- a/CHEWBBACA/utils/parameters_validation.py
+++ b/CHEWBBACA/utils/parameters_validation.py
@@ -1316,18 +1316,19 @@ def check_unique_prefixes(input_list):
 	"""
 	input_paths = fo.read_lines(input_list)
 	basenames = [fo.file_basename(file) for file in input_paths]
-	unique_ids = [fo.split_joiner(name, [0], '.') for name in basenames]
+	unique_ids = {}
+	for name in basenames:
+		prefix = fo.split_joiner(name, [0], '.')
+		unique_ids.setdefault(prefix, []).append(name)
 
 	# Detect if some inputs share the same unique prefix
 	if len(set(unique_ids)) < len(input_paths):
-		basename_counts = [[name, basenames.count(name)]
-							for name in set(basenames)]
-		repeated_basenames = ['{0}: {1}'.format(*l)
-								for l in basename_counts if l[1] > 1]
-		sys.exit('\nSome input files share the same filename prefix '
-				'(substring before the first "." in the filename). '
-				'Please make sure that every input file has a unique '
-				'filename prefix.\n{0}'.format('\n'.join(repeated_basenames)))
+		repeated_basenames = [v for k, v in unique_ids.items() if len(v) > 1]
+		repeated_basenames = [','.join(l) for l in repeated_basenames]
+		sys.exit('The following input files share the same filename prefix '
+				 '(substring before the first "." in the filename):\n{0}\n'
+				 'Please ensure that every input file has a unique '
+				 'filename prefix.'.format('\n'.join(repeated_basenames)))
 
 	return False
 
@@ -1354,7 +1355,7 @@ def check_blanks(input_list):
 	include_blanks = [name for name in basenames if ' ' in name]
 
 	if len(include_blanks) > 0:
-		sys.exit('\nThe following input files include blank spaces '
+		sys.exit('The following input files include blank spaces '
 				 'in the filename:\n{0}\nPlease ensure that filenames '
 				 'do not include blank spaces or special characters '
 				 '(e.g. !@#?$^*()+)'.format('\n'.join(include_blanks)))
diff --git a/CITATION.cff b/CITATION.cff
index 4d0f0b25..f8c4d5ff 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -13,7 +13,7 @@ authors:
     given-names: João
   - family-names: Ramirez
     given-names: Mário
-version: 3.3.0
+version: 3.3.4
 date-released: "2023-06-29"
 keywords:
   - bioinformatics
diff --git a/pyproject.toml b/pyproject.toml
index 3360a4c1..5c9ca16b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "chewBBACA"
-version = "3.3.3"
+version = "3.3.4"
 requires-python = ">=3.8"
 dependencies = [
     "numpy~=1.24.3",