Question: Restart Galaxy and jobs failed because of missing tmp file
gravatar for xiao2
21 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 • 617 views
ADD COMMENTlink written 21 months ago by xiao210
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