diff --git a/src/graphnet/data/utilities/sqlite_utilities.py b/src/graphnet/data/utilities/sqlite_utilities.py
index cfa308ba2..8764bae3c 100644
--- a/src/graphnet/data/utilities/sqlite_utilities.py
+++ b/src/graphnet/data/utilities/sqlite_utilities.py
@@ -46,6 +46,8 @@ def get_primary_keys(database: str) -> Tuple[Dict[str, str], str]:
         query = 'SELECT name FROM sqlite_master WHERE type == "table"'
         table_names = [table[0] for table in conn.execute(query).fetchall()]
 
+        assert len(table_names) > 0, "No tables found in database."
+
         integer_primary_key = {}
         for table in table_names:
             query = f"SELECT l.name FROM pragma_table_info('{table}') as l WHERE l.pk = 1;"
diff --git a/src/graphnet/data/writers/sqlite_writer.py b/src/graphnet/data/writers/sqlite_writer.py
index ab8d95051..ab4b32094 100644
--- a/src/graphnet/data/writers/sqlite_writer.py
+++ b/src/graphnet/data/writers/sqlite_writer.py
@@ -160,7 +160,14 @@ def _merge_databases(
         for file_count, input_file in tqdm(enumerate(files), colour="green"):
 
             # Extract table names and index column name in database
-            tables, primary_key = get_primary_keys(database=input_file)
+            try:
+                tables, primary_key = get_primary_keys(database=input_file)
+            except AssertionError as e:
+                if "No tables found in database." in str(e):
+                    self.warning(f"Database {input_file} is empty. Skipping.")
+                    continue
+                else:
+                    raise e
 
             for table_name in tables.keys():
                 # Extract all data in the table from the given database