Question: Issue with running TOphat 2 on local galaxy with Rsync genomes
0
gravatar for onspotproductions
22 months 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/local.py", line 128, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta
    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.7/subprocess.py", line 524, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
assembly galaxy rna-seq • 554 views
ADD COMMENTlink written 22 months ago by onspotproductions40
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