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 <m.bernt@ufz.de> 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, m.bernt@ufz.de, www.ufz.de
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