diff --git a/pypiper/pipeline.py b/pypiper/pipeline.py
index ab3f8d9..a02c9ad 100644
--- a/pypiper/pipeline.py
+++ b/pypiper/pipeline.py
@@ -336,8 +336,9 @@ def run(self, start_point=None, stop_before=None, stop_after=None):
                 stage.run()
             except Exception as e:
                 self.manager._triage_error(e, nofail=stage.nofail)
+            else:
+                self.checkpoint(stage)
             self.executed.append(stage)
-            self.checkpoint(stage)
 
         # Add any unused stages to the collection of skips.
         self.skipped.extend(self._stages[stop_index:])