diff --git a/pull_into_place/commands/02_setup_model_fragments.py b/pull_into_place/commands/02_setup_model_fragments.py
index 313ccad..971f97c 100644
--- a/pull_into_place/commands/02_setup_model_fragments.py
+++ b/pull_into_place/commands/02_setup_model_fragments.py
@@ -39,8 +39,6 @@ def main():
 
     workspace = pipeline.RestrainedModels(args['<workspace>'])
     workspace.check_paths()
-    workspace.make_dirs()
-    workspace.clear_fragments()
 
     # Run the fragment generation script.
 
@@ -58,4 +56,6 @@ def main():
     if args['--dry-run']:
         print ' '.join(generate_fragments)
     else:
+        workspace.make_dirs()
+        workspace.clear_fragments()
         subprocess.call(generate_fragments)
diff --git a/pull_into_place/commands/07_setup_design_fragments.py b/pull_into_place/commands/07_setup_design_fragments.py
index 2318e44..28b5bcb 100644
--- a/pull_into_place/commands/07_setup_design_fragments.py
+++ b/pull_into_place/commands/07_setup_design_fragments.py
@@ -33,8 +33,6 @@ def main():
     workspace = pipeline.ValidatedDesigns(args['<workspace>'], args['<round>'])
     workspace.check_paths()
     workspace.check_rosetta()
-    workspace.make_dirs()
-    workspace.clear_fragments()
 
     # Run the fragment generation script.
 
@@ -49,5 +47,7 @@ def main():
     if args['--dry-run']:
         print ' '.join(generate_fragments)
     else:
+        workspace.make_dirs()
+        workspace.clear_fragments()
         subprocess.call(generate_fragments)