Question: Issue with running TOphat 2 on local galaxy with Rsync genomes
gravatar for onspotproductions
2.3 years ago by
United States
onspotproductions40 wrote:

I attempted to run a test job on our new local galaxy instance and generated an error when attempting to align RNA reads to HG19 using tophat 2. I have never encountered this issue before.

Traceback (most recent call last):
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/runners/", line 128, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/", line 1257, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/datatypes/", line 339, in set_meta
    exit_code = args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.7/", line 524, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib64/python2.7/", line 711, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
assembly galaxy rna-seq • 663 views
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