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
galaxy-dev@lists.galaxyproject.org