miBig downloads #300
Description
Are you using the latest release?
yes
Describe the bug
miBig URLs seem to have changed?
https://mibig.secondarymetabolites.org/#!/download lists the FASTA download as
https://dl.secondarymetabolites.org/mibig/mibig_json_1.4.tar.gz
but the URL in library.py is
lib/library.py:183: 'mibig': 'https://mibig.secondarymetabolites.org/MIBiG_prot_seqs_1.4.fasta',
I think need to email them - all the FASTA links are also to JSON downloads for all versions so maybe something changed on their end. Contact link doesn't give a contact page but I emailed help@secondarymetabolites.org and await a response.
What command did you issue?
funannotate setup -u -i mibig
Logfiles
funannotate setup -u -i mibig
-------------------------------------------------------
[09:50 AM]: OS: linux2, 16 cores, ~ 132 GB RAM. Python: 2.7.12
[09:50 AM]: Running funannotate v1.6.0-2fe943e
[09:50 AM]: Database location: /opt/linux/centos/7.x/x86_64/pkgs/funannotate/share
[09:50 AM]: Checking for newer versions of database files
Traceback (most recent call last):
File "/bigdata/operations/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/funannotate/git-live/bin/funannotate-setup.py", line 453, in <module>
mibigDB(DatabaseInfo, args.force)
File "/bigdata/operations/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/funannotate/git-live/bin/funannotate-setup.py", line 295, in mibigDB
if check4newDB('mibig', info):
File "/bigdata/operations/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/funannotate/git-live/bin/funannotate-setup.py", line 55, in check4newDB
newmd5 = calcmd5remote(lib.DBURL.get(name))
File "/bigdata/operations/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/funannotate/git-live/bin/funannotate-setup.py", line 33, in calcmd5remote
remote = urllib2.urlopen(url)
File "/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/envs/funannotate/lib/python2.7/urllib2.py", line 154, in urlopen
return opener.open(url, data, timeout)
File "/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/envs/funannotate/lib/python2.7/urllib2.py", line 435, in open
response = meth(req, response)
File "/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/envs/funannotate/lib/python2.7/urllib2.py", line 548, in http_response
'http', request, response, code, msg, hdrs)
File "/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/envs/funannotate/lib/python2.7/urllib2.py", line 473, in error
return self._call_chain(*args)
File "/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/envs/funannotate/lib/python2.7/urllib2.py", line 407, in _call_chain
result = func(*args)
File "/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/envs/funannotate/lib/python2.7/urllib2.py", line 556, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
urllib2.HTTPError: HTTP Error 404: Not Found
OS/Install Information
- output of
funannotate check --show-versions