Hi,
All our workflows with TopHat finished with status: "tool error" & "Unable to
finish job".
We tested them on Galaxy 15.11 and 16.01 (latest works with python 2.6).
Our batch system is SGE. TopHat is v2.0.14 revision 4eb3c3beb9c7
TopHat calculations on the cluster are fine and finished without any errors but
during the running set_metadata_XYZ.py script (which is also called from
submited script) job fails and reports above mentioned error status.
Logs are:
galaxy.jobs.runners.drmaa DEBUG 2016-05-19 13:53:18,054 (481/1533559) state
change: job finished normally
galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool
progress
galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool
progress
galaxy.datatypes.metadata DEBUG 2016-05-19 13:53:21,759 setting metadata
externally failed for HistoryDatasetAssociation 1965: [Errno2] No such file or
directory
galaxy.jobs.runners ERROR 2016-05-19 13:53:24,367 (481/1533559) Job wrapper
finish method failed
Traceback (most recent call last):
File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/runners/__init__.py", line 590,
in finish_job
job_state.job_wrapper.finish( stdout, stderr, exit_code )
File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/__init__.py", line 1221, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
File "/ptmp/galaxy1/galaxy/lib/galaxy/datatypes/binary.py", line 314, in
set_meta
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb'
) )
File "/usr/lib64/python2.6/subprocess.py", line 470, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib64/python2.6/subprocess.py", line 623, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1141, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
As I understand Galaxy operates with pickle data ( which were saved before
submiting job in file with id 1965:
metadata_in_HistoryDatasetAssociation_1965_sPyPfZ )
during running function set_metadata() and does not find some files and exit
with error message [false, "[Errno 2] No such file or directory"] writen to the
file metadata_results_HistoryDatasetAssociation_1965_k5I9PM and kill job.
What causes this error and how to fix this behavior?
Thanx in advance,
Nick
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