I noticed a strange behaviour in our local galaxy installation. First of all, my universe_wsgi.ini contains "retry_metadata_internally = False" and "cleanup_job = always". The tool writes its output simply into the job_working_directory and we move it via && mv static_filename.txt $output in the <command>-tag. This works fine.
When restarting the galaxy server and executing the tool after a fresh restart, everything is ok, there are no errors.
When executing the same tool a second time, galaxy brings a "tool error" stating that it was unable to finish the job. Nevertheless, the output files are all correct (but marked as red or failed).
The error report states:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 997, in finish
if ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and self.app.config.retry_metadata_internally ):
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 731, in external_metadata_set_successfully
rval, rstring = json.load( open( metadata_files.filename_results_code ) )
IOError: [Errno 2] No such file or directory: u'/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0'
And in the logfile you can find multiple entries like that:
galaxy.datatypes.metadata DEBUG 2014-06-25 14:29:35,466 Failed to cleanup external metadata file (filename_results_code) for HistoryDatasetAssociation_281: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0'
The if-statement in /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 997 should evaluate to False, since self.app.config.retry_metadata_internally is set to False in the universe_wsgi.ini but it seems it doesn't in this case?
Anyone having experienced such a behavior? Any suggestions how to go on and solve the issue?