diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 0ffc29ae223..da14c39d994 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -752,7 +752,10 @@ class JobWrapper( object ):
         sizes = []
         output_paths = self.get_output_fnames()
         for outfile in [ str( o ) for o in output_paths ]:
-            sizes.append( ( outfile, os.stat( outfile ).st_size ) )
+            if os.path.exists( outfile ):
+                sizes.append( ( outfile, os.stat( outfile ).st_size ) )
+            else:
+                sizes.append( ( outfile, 0 ) )
         return sizes
 
     def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, set_extension = True, **kwds ):
@@ -999,7 +1002,10 @@ class TaskWrapper(JobWrapper):
         sizes = []
         output_paths = self.get_output_fnames()
         for outfile in [ str( o ) for o in output_paths ]:
-            sizes.append( ( outfile, os.stat( outfile ).st_size ) )
+            if os.path.exists( outfile ):
+                sizes.append( ( outfile, os.stat( outfile ).st_size ) )
+            else:
+                sizes.append( ( outfile, 0 ) )
         return sizes
 
     def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, set_extension = True, **kwds ):
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index a5faa8439d2..8a33f96faf4 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -323,12 +323,14 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
         for i, dataset in enumerate( data_list ):
             job.add_output_library_dataset( 'output%i' % i, dataset )
             # Create an empty file immediately
-            open( dataset.file_name, "w" ).close()
+            if not dataset.dataset.external_filename:
+                open( dataset.file_name, "w" ).close()
     else:
         for i, dataset in enumerate( data_list ):
             job.add_output_dataset( 'output%i' % i, dataset )
             # Create an empty file immediately
-            open( dataset.file_name, "w" ).close()
+            if not dataset.dataset.external_filename:
+                open( dataset.file_name, "w" ).close()
     job.state = job.states.NEW
     trans.sa_session.add( job )
     trans.sa_session.flush()