Hi Matthias, any chance https://github.com/galaxyproject/galaxy/pull/4644 would fix this for you ?
Best, Marius On 16 October 2017 at 20:12, Matthias Bernt <[email protected]> wrote: > Dear list, > > today I got an erroneous result (red) despite the output of the tool to be > seems fine. Seemingly there was an error during setting the metadata. > > ``` > Fatal error: An error occured during execution, see stderr and stdout for > more information > Reading reference gene model /gpfs1/data/galaxy_server/gala > xy-dev/database/files/002/dataset_2992.dat ... Done > Loading SAM/BAM file ... Finished > Total 62188 usable reads were sampled > Traceback (most recent call last): > File > "/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py", > line 1, in > from galaxy_ext.metadata.set_metadata import set_metadata; > set_metadata() > File > "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py", > line 85, in set_metadata > datatypes_registry.load_datatypes(root_dir=galaxy_root, > config=datatypes_config) > File > "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py", > line 109, in load_datatypes > tree = galaxy.util.parse_xml(config) > File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", > line 214, in parse_xml > root = tree.parse(fname, parser=ElementTree.XMLParser(t > arget=DoctypeSafeCallbackTarget())) > File > "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py", > line 647, in parse > source = open(source, "rb") > IOError: [Errno 2] No such file or directory: > '/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW' > ``` > > Are there any suggestions how to continue with such a behavior. The file > system on our cluster seems to be slow at the moment, could this be the > cause? > > Best, > Matthias > > > -- > > ------------------------------------------- > Matthias Bernt > Bioinformatics Service > Molekulare Systembiologie (MOLSYB) > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > Helmholtz Centre for Environmental Research GmbH - UFZ > Permoserstraße 15, 04318 Leipzig, Germany > <https://maps.google.com/?q=Permoserstra%C3%9Fe+15,+04318+Leipzig,+Germany&entry=gmail&source=g> > Phone +49 341 235 482296, > [email protected], www.ufz.de > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig > Wilfried Kraus > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Dr. h.c. Georg Teutsch > Administrative Geschäftsführerin/ Administrative Managing Director: > Prof. Dr. Heike Graßmann > ------------------------------------------- > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/
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