Dear all,
we are currently working on a new local Galaxy instance (17.01) and we encounter an error when running bwa-mem jobs. The jobs fail with a python subprocess OSError triggered in the module lib/galaxy/datatypes/
Here is the traceback:
Traceback (most recent call last):
  File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/", line 624, in finish_job
    job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/opt/galaxy/galaxy/lib/galaxy/jobs/", line 1350, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/opt/galaxy/galaxy/lib/galaxy/datatypes/", line 391, 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
Has anyone seen this error before? Is there anything we can do to get rid of it?

Thanks a lot!


Georgios Nikolis
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
phone: +49 6221 42-4659


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537