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/galaxy-dev/database/files/002/data set_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/metadat a/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(target=DoctypeSafeCallbackTarge t()))
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
Phone +49 341 235 482296,
m.bernt@ufz.de, 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
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