diff --git a/pytype/tools/analyze_project/main.py b/pytype/tools/analyze_project/main.py
index 4eab45f4c..4010c66dd 100755
--- a/pytype/tools/analyze_project/main.py
+++ b/pytype/tools/analyze_project/main.py
@@ -75,13 +75,16 @@ def main():
     import_graph = importlab.graph.ImportGraph.create(
         env, conf.inputs, trim=True)
     unreadable_inputs = conf.inputs & import_graph.unreadable_files
-    assert not unreadable_inputs, '\n  '.join(
+    unreadable_python_inputs = {filename for filename in unreadable_inputs if filename.endswith('.py')}
+    assert not unreadable_python_inputs, '\n  '.join(
         ['Unparseable in Python %s:' % conf.python_version] +
-        sorted(unreadable_inputs))
+        sorted(unreadable_python_inputs))
   except Exception as e:  # pylint: disable=broad-except
-    logging.critical('Cannot parse input files:\n%s', str(e))
+    logging.critical('Cannot parse input files:\n%s', e)
     sys.exit(1)
 
+  conf.inputs -= unreadable_inputs
+
   if args.tree:
     print('Source tree:')
     importlab.output.print_tree(import_graph)