Below is an error obtained from our galaxy install. We have custom directories sets for the files directory and the jobs directory. Galaxy appears to move the files but then attempts to look for them at the original path. I have tried unsetting these options but the issue of it looking in the jobs_directory after the file has already been moved still persists.
galaxy.jobs DEBUG 2017-11-24 17:53:19,057 finish(): Moved /var/web_services/galaxy/database/jobs_directory/000/320/galaxy_dataset_431.dat to /mnt/ceph/home/galaxy/galaxy/files_directory/000/dataset_401.dat galaxy.model.metadata DEBUG 2017-11-24 17:53:19,128 setting metadata externally failed for HistoryDatasetAssociation 431: [Errno 2] No such file or directory galaxy.jobs.runners ERROR 2017-11-24 17:53:19,319 (320/179084) Job wrapper finish method failed Traceback (most recent call last): File "/var/web_services/galaxy/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/var/web_services/galaxy/lib/galaxy/jobs/__init__.py", line 1266, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/var/web_services/galaxy/lib/galaxy/datatypes/binary.py", line 391, 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 galaxy.jobs ERROR 2017-11-24 17:53:19,337 fail(): Missing output file in working directory: [Errno 2] No such file or directory: '/var/web_services/galaxy/database/jobs_directory/000/320/galaxy_dataset_431.dat'