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Question: IOError: [Errno 2] No such file or directory: '/galaxy-repl/main/scratch2/tmppqOf7j'
0
gravatar for annamariabugaj
15 months ago by
annamariabugaj • 0
annamariabugaj • 0 wrote:

I am trying to do statistics and get this error:

Traceback (most recent call last): File "/galaxy-repl/main/jobdir/016/527/16527280/set_metadata__PUIn7.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 85, in set_metadata datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config ) File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 104, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/__init__.py", line 214, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/cvmfs/main.galaxyproject.org/python/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/galaxy-repl/main/scratch2/tmppqOf7j'
software error • 744 views
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by annamariabugaj • 0
1
gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This error was due to brief cluster problem that has been corrected. Please rerun any jobs that failed during this time.

Thanks for reporting the problem! Jen, Galaxy team
ADD COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

Dear Jenn,

Can you please be so kind to share your solution? I have the same issue on my galaxy cluster and it's very annoying. I have no idea how to solve it! We tried to add "-noac" param to NFS (performance was terrible), increase "retry_job_output_collection" in galaxy.ini, but nothing helped.

Thanks, Marija

ADD REPLY • link written 13 months ago by marija.djurdjevic • 30
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