Hi Nate, I tried to run the tool with a small input file. Then that case also the test fails and returns the same error message. FAIL: mGenePredict ( mgenepredict ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 114, in test_tool self.do_it() File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 54, in do_it self.verify_dataset_correctness( file ) File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 323, in verify_dataset_correctness if wait: self.wait() #wait for job to finish File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 617, in wait self.assertNotEqual(count, maxiter) AssertionError: 20 == 20 Also I can find that the job is not finished even though I got the fail message. I confirmed the same, when I run the test again it produces an error message stating that the Galaxy port is already in use. I hope my assumption is true, if not please let me know. Many thanks, Vipin T S