diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 5daf9a79425..324a291d801 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -99,7 +99,7 @@ class Bam( Binary ):
         stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
         command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name )
         proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
-        
+        proc.wait()
         #Did index succeed?
         stderr = open( stderr_name ).read().strip()
         if stderr:
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 2d191d2fd4e..41c49d0dc36 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -118,7 +118,10 @@ def check_zip( temp_name ):
     # 1. Archives can only include .ab1, .scf or .txt files
     # 2. All file extensions within an archive must be the same
     name = zip_file.namelist()[0]
-    test_ext = name.split( "." )[1].strip().lower()
+    try:
+        test_ext = name.split( "." )[1].strip().lower()
+    except:
+        return ( True, False, None )
     if not ( test_ext in unsniffable_binary_formats or test_ext == 'txt' ):
         return ( True, False, test_ext )
     for name in zip_file.namelist():