diff --git a/src/wic/api/pythonapi.py b/src/wic/api/pythonapi.py
index 9ccf7899..fd396455 100644
--- a/src/wic/api/pythonapi.py
+++ b/src/wic/api/pythonapi.py
@@ -585,6 +585,7 @@ def write_ast_to_disk(self, directory: Path) -> None:
         yaml_contents = {"inputs": inputs, "steps": steps} if inputs else {"steps": steps}
         # NOTE: For various reasons, process_name should be globally unique.
         # In this case, it is to avoid overwriting files.
+        directory.mkdir(exist_ok=True, parents=True)
         with open(str(directory / self.process_name) + '.wic', mode='w', encoding='utf-8') as f:
             f.write(yaml.dump(yaml_contents, sort_keys=False, line_break='\n', indent=2))
 
@@ -755,7 +756,7 @@ def run(self) -> None:
             input_output.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
 
         # Do NOT capture stdout and/or stderr and pipe warnings and errors into a black hole.
-        retval = run_local_module.run_local(args, rose_tree, args.cachedir, 'cwltool', False)
+        retval = run_local_module.run_local(args, rose_tree, args.cachedir, 'cwltool', True)
 
         # Finally, since there is an output file copying bug in cwltool,
         # we need to copy the output files manually. See comment above.