I am indexing reference genomes for bowtie2/tophat2, using the
corresponding data manager. I am getting some successful indexes and others
are giving an error. For the successful ones I see the genomes are
appearing in the "built in index" drop down for both bowtie2 and tophat2.
For the unsuccessful ones I am seeing them in the bowtie2 drop down but not
tophat2. Any ideas on what could be causing this issue?

The error message is as follows

Thanks in advance.

Traceback (most recent call last):
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 128, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 1375, in finish
    self.tool.exec_after_process( self.queue.app, inp_data, out_data,
param_dict, job=job )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py",
line 2107, in exec_after_process
    data_manager.process_result( out_data )
line 303, in process_result
    self.process_move( data_table_name, name, output_ref_values[ name
].extra_files_path, **data_table_value )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/model/__init__.py",
line 1891, in extra_files_path
    return self.dataset.extra_files_path
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/model/__init__.py",
line 1707, in get_extra_files_path
    return self.object_store.get_filename( self, dir_only=True,
extra_dir=self._extra_files_path or "dataset_%d_files" % self.id )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
line 487, in get_filename
    return self._call_method('get_filename', obj, ObjectNotFound,
True, **kwargs)
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
line 508, in _call_method
    % ( method, str( obj ), str( kwargs ) ) )
ObjectNotFound: objectstore, _call_method failed: get_filename on
<galaxy.model.Dataset object at 0x7f2584803590>, kwargs: {'dir_only':
True, 'extra_dir': 'dataset_19568_files'}
Tool execution generated the following error message:
Unable to finish job
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