question-mark
Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Issue download protozoa genomes

See original GitHub issue

Same 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:closed
  • Created 3 years ago
  • Comments:8 (6 by maintainers)

github_iconTop GitHub Comments

1reaction
kblincommented, Jun 18, 2020

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.

0reactions
kblincommented, Jun 19, 2020
Read more comments on GitHub >

github_iconTop Results From Across the Web

Protozoan genomes - data download
Protozoan genomes - data download. This page provides access to genomes sequenced at the Wellcome Sanger Institute. We make all our sequence data...
Read more >
Genomes Download (FTP) FAQ - NCBI
The genome download service in the Assembly resource makes it easy to download data for multiple genomes without having to write scripts.
Read more >
Protozoan genomes: gene identification and annotation
Volume 35, Issue 5, 30 April 2005, Pages 495-512 ... The draft sequence of several complete protozoan genomes is now available and genome...
Read more >
(PDF) Protozoan genomes: Gene identification and annotation
PDF | The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing ... Download full-text PDF.
Read more >
Extremely Streamlined Macronuclear Genome in the Free ...
Next, we compared the genome size with all published protozoan genomes and found that F. salina has the smallest genome among all ...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found