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/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(target=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
Phone +49 341 235 482296,
m.be...@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
-------------------------------------------
___________________________________________________________
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/
