Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

unable to download mlst schemes #264

Closed
samlipworth opened this issue Apr 17, 2019 · 2 comments
Closed

unable to download mlst schemes #264

samlipworth opened this issue Apr 17, 2019 · 2 comments

Comments

@samlipworth
Copy link

Traceback (most recent call last):
File "/usr/local/bin/ariba", line 4, in
import('pkg_resources').run_script('ariba==2.13.4', 'ariba')
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 742, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1503, in run_script
exec(code, namespace, namespace)
File "/usr/local/lib/python3.6/dist-packages/ariba-2.13.4-py3.6-linux-x86_64.egg/EGG-INFO/scripts/ariba", line 310, in
args.func(args)
File "/usr/local/lib/python3.6/dist-packages/ariba-2.13.4-py3.6-linux-x86_64.egg/ariba/tasks/pubmlstget.py", line 11, in run
preparer.run()
File "/usr/local/lib/python3.6/dist-packages/ariba-2.13.4-py3.6-linux-x86_64.egg/ariba/pubmlst_ref_preparer.py", line 75, in run
pubmlst = pubmlst_getter.PubmlstGetter(debug=self.debug, verbose=self.verbose)
File "/usr/local/lib/python3.6/dist-packages/ariba-2.13.4-py3.6-linux-x86_64.egg/ariba/pubmlst_getter.py", line 19, in init
self.xml_tree = self._get_xml_file_tree()
File "/usr/local/lib/python3.6/dist-packages/ariba-2.13.4-py3.6-linux-x86_64.egg/ariba/pubmlst_getter.py", line 28, in _get_xml_file_tree
self._download_file(xml_url, xml_file)
File "/usr/local/lib/python3.6/dist-packages/ariba-2.13.4-py3.6-linux-x86_64.egg/ariba/pubmlst_getter.py", line 50, in _download_file
raise Error('Error downloading: ' + url)
ariba.pubmlst_getter.Error: Error downloading: http://pubmlst.org/data/dbases.xml

@samlipworth
Copy link
Author

I have tried this in several ways - perhaps is is related to the file on pubmlst which actually appears to be empty. I have been able to execute this function successfuly in the past..

@samlipworth
Copy link
Author

This was due to an error with the pubmlst site - the dbases.xml file was empty because of a server error in Oxford's zoology dept - this is now fixed and so I am closing this.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant