Question: Restart Galaxy and jobs failed because of missing tmp file
gravatar for xiao2
11 months ago by
xiao210 wrote:


I installed Galaxy 16.10 on a server, and trying to run some jobs with condor runner, I need to restart the Galaxy service sometimes when there are running jobs, in the past (older Galaxy version) I didn't have any problem because the jobs are managed by condor. But now if there are running jobs when I restart Galaxy, I got the following error message for the jobs when they finish:

Traceback (most recent call last): File "/opt/galaxy/database/jobs_directory/000/30/", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/opt/galaxy/lib/galaxy_ext/metadata/", line 85, in set_metadata datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config ) File "/opt/galaxy/lib/galaxy/datatypes/", line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/opt/galaxy/lib/galaxy/util/", line 214, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/lib/python2.7/xml/etree/", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/opt/galaxy/database/tmp/tmpLqb7Le'

Please let me know if you have any clue how to fix this.

Thanks in advance, Mark

galaxy • 367 views
ADD COMMENTlink written 11 months ago by xiao210
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 117 users visited in the last hour