liftOver functional tests failed - galaxy-dev

16 Feb 2015


      Dear All,
I am still trying to migrate my production server to new hardware and would like to have all functional tests pass before turning off my old server.
I am facing an issue with liftOver functional tests, they failed when running 'sh run_tests.sh -id liftOver1' on the command line with these errors:
======================================================================
ERROR: test_tool_000000 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool
    self.do_it( td )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it
    data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool
    raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}}
-------------------- >> begin captured logging << --------------------
======================================================================
ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) > Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool
    self.do_it( td )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it
    data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool
    raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}}
-------------------- >> begin captured logging << --------------------
======================================================================
ERROR: test_tool_000002 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) > Test-3
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool
    self.do_it( td )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it
    data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool
    raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}}
-------------------- >> begin captured logging << --------------------
======================================================================
ERROR: test_tool_000003 (functional.test_toolbox.TestForTool_liftOver1)
Convert genome coordinates ( liftOver1 ) > Test-4
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool
    self.do_it( td )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it
    data_list, jobs = galaxy_interactor.run_tool( testdef, test_history )
  File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool
    raise Exception( datasets_object[ 'message' ] )
Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}}
-------------------- >> begin captured logging << --------------------
But when tested using the GUI, they did pass.
I have configured the alignseq.loc and liftOver.loc, they both contained TAB delimited data and file locations have been checked.
I’ve downloaded 5.bed into the GUI, used for testing liftOver, and configure the parameters according to those set in the test:
    <test>
      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
      <param name="to_dbkey" value="panTro2" />
      <param name="minMatch" value="0.95" />
      <param name="choice" value="0" />
      <output name="out_file1" file="5_liftover_mapped.bed"/>
      <output name="out_file2" file="5_liftover_unmapped.bed"/>
    </test>
[cid:5D5398C5-3D95-4074-9A86-81486A8CD20F@cri.camres.org]
[cid:45B5289B-C7A8-46CE-A5B2-C879D26B1D18@cri.camres.org]
And here are the results:
[cid:D4910E74-8A0E-4C58-9D17-46C37DEAF99F@cri.camres.org]
Any ideas of what could be that the functional tests on the command line failed? Any help to where to look would be greatly appreciated. Many thanks in advance.
Best wishes,
Anne.
--
Dr Anne Pajon - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pajon@cruk.cam.ac.ukmailto:anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631