Well that is no good - I take it you have outputs_to_working_directory set to True in your galaxy.ini? That option doesn't get a lot of testing and it seems like it is interfering with retry_metadata_internally = True. What version of Galaxy are you running? Another work around would be to try to figure out why you need to retry_metadata_internally to start with - it shouldn't be needed - in this case it looks like maybe samtools wasn't available on the cluster where this ran. Putting that on the Galaxy PATH might help - I'm not sure. I've created a Github issue here (https://github.com/galaxyproject/galaxy/issues/5097). Sorry about this. -John On Fri, Nov 24, 2017 at 5:57 PM, Evan Clark <eclark28@my.fau.edu> wrote:

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 it 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' ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

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