Issue download protozoa genomes
See original GitHub issueSame issue as in #118
Running version 0.2.12 installed from conda
Command is
ncbi-genome-download --section genbank --format fasta protozoa
How do I get the fix?
Traceback (most recent call last):
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/bin/ncbi-genome-download", line 6, in <module>
exit(main())
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/ncbi_genome_download
/__main__.py", line 25, in main
ret = args_download(args)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/ncbi_genome_download
/core.py", line 159, in args_download
return config_download(config)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/ncbi_genome_download
/core.py", line 196, in config_download
curr_jobs = create_downloadjob(entry, group, config)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/ncbi_genome_download
/core.py", line 397, in create_downloadjob
checksums = grab_checksums_file(entry)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/ncbi_genome_download
/core.py", line 465, in grab_checksums_file
req = requests.get(full_url)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/requests/api.py", li
ne 76, in get
return request('get', url, params=params, **kwargs)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/requests/api.py", li
ne 61, in request
return session.request(method=method, url=url, **kwargs)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/requests/sessions.py
", line 516, in request
prep = self.prepare_request(req)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/requests/sessions.py
", line 449, in prepare_request
p.prepare(
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/requests/models.py",
line 314, in prepare
self.prepare_url(url, params)
File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/ncbi-genome-download/lib/python3.8/site-packages/requests/models.py",
line 388, in prepare_url
raise MissingSchema(error)
requests.exceptions.MissingSchema: Invalid URL 'na/md5checksums.txt': No schema supplied. Perhaps you meant http://na/md5checksums.txt?
Issue Analytics
- State:
- Created 3 years ago
- Comments:8 (6 by maintainers)
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Top GitHub Comments
Yeah, it’s the same issue as #118, that’s fixed in master by #114, but I didn’t get around to relase the new version with that fix yet.
Bioconda version is in progress: https://github.com/bioconda/bioconda-recipes/pull/22778