Merge pull request #304 from nextstrain/refine_exception

Handle Missing/Empty file Error in Refine
nextstrain · Jul 1, 2019 · 1e37b86 · 1e37b86
2 parents 33ad4ef + 99f87fa
commit 1e37b86
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/augur/refine.py b/augur/refine.py
@@ -133,10 +133,11 @@ def run(args):
             T = Phylo.read(args.tree, fmt)
             node_data['input_tree'] = args.tree
             break
-        except:
-            pass
+        except Exception as error:
+            print("\n\nERROR: reading tree from %s failed: %s" % (args.tree, error))
+            return 1
     if T is None:
-        print("ERROR: reading tree from %s failed."%args.tree)
+        print("\n\nERROR: reading tree from %s failed."%args.tree)
         return 1
 
     if not args.alignment: