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