diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper.py
index c4501f2183c..043b6e57083 100644
--- a/tools/metag_tools/megablast_wrapper.py
+++ b/tools/metag_tools/megablast_wrapper.py
@@ -81,6 +81,8 @@ def __main__():
         output.write( "%s\n" % new_line )
     output.close()
     
+    os.unlink( mega_temp_output ) #remove the tempfile that we just reformated the contents of
+    
     if invalid_lines:
         print "Unable to parse %d lines. Keep the default format." % invalid_lines
         
@@ -91,4 +93,4 @@ def __main__():
             print line
         os.remove( './error.log' )
     
-if __name__ == "__main__" : __main__()
\ No newline at end of file
+if __name__ == "__main__" : __main__()