diff --git a/src/hdf5_writer.py b/src/hdf5_writer.py
index a990b22..3006b7e 100644
--- a/src/hdf5_writer.py
+++ b/src/hdf5_writer.py
@@ -184,11 +184,11 @@ def create_hdf5_file_from_filesystem_path(path_to_input_directory: str,
                 group_name = dirpath.replace(os.sep,'/')
                 group_name = group_name.replace(root_dir.replace(os.sep,'/') + '/', '/')
 
-                # Flatten group name to one level
+                # Flatten group name to two level
                 if select_dir_keywords:
                     offset = sum([len(i.split(os.sep)) if i in dirpath else 0 for i in select_dir_keywords])
                 else:
-                    offset = 1
+                    offset = 2
                 tmp_list = group_name.split('/')
                 if len(tmp_list) > offset+1:
                     group_name = '/'.join([tmp_list[i] for i in range(offset+1)])