diff --git a/bob/bio/base/tools/command_line.py b/bob/bio/base/tools/command_line.py
index df62b19ae481d5f06f0eee7e99a243fb658fdfc8..6764792663af1ce5fa3b24e4e87b978773f95f09 100644
--- a/bob/bio/base/tools/command_line.py
+++ b/bob/bio/base/tools/command_line.py
@@ -246,7 +246,7 @@ def initialize(parsers, command_line_parameters = None, skips = []):
     preprocessed_directory = os.path.join(args.temp_directory, args.preprocessed_directory),
     extracted_directory = os.path.join(args.temp_directory, extractor_sub_dir, args.extracted_directory),
     projected_directory = os.path.join(args.temp_directory, projector_sub_dir, args.projected_directory),
-    model_directories = [os.path.join(args.temp_directory, protocol, m) for m in args.model_directories],
+    model_directories = [os.path.join(args.temp_directory, model_sub_dir, m) for m in args.model_directories],
     score_directories = [os.path.join(args.result_directory, protocol, z) for z in args.score_directories],
     zt_score_directories = [os.path.join(args.temp_directory, protocol, s) for s in args.zt_directories],
     compressed_extension = '.tar.bz2' if args.write_compressed_score_files else '',