sokrypton / sokrypton/ColabFold
403 Forbidden message from API
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Description
We received the following message when running colabfold_batch on a single small test sequence. We get this same result on two different compute clusters. Does this mean our IPs are banned?
Command: colabfold_batch --num-models 1 --stop-at-score 2 ./6A5J.fasta ./output
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2024-11-04 14:04:16,767 Server didn't reply with json: <html>
<head><title>403 Forbidden</title></head>
<body>
<center><h1>403 Forbidden</h1></center>
<hr><center>nginx</center>
</body>
</html>
2024-11-04 14:04:16,771 Could not get MSA/templates for 6A5J: MMseqs2 API is giving errors. Please confirm your input is a v
alid protein sequence. If error persists, please try again an hour later.
Traceback (most recent call last):
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py", line 1467,
in run
= get_msa_and_templates(jobname, query_sequence, a3m_lines, result_dir, msa_mode, use_templates,
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py", line 827, i
n get_msa_and_templates
a3m_lines = run_mmseqs2(
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/colabfold/colabfold.py", line 21
0, in run_mmseqs2
raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists
, please try again an hour later.')
Exception: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please tr
y again an hour later.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the colabfold_batch command and inspect colabfold/batch.py around get_msa_and_templates and colabfold/colabfold.py around run_mmseqs2. Determine whether the MMseqs2 API 403 is caused by the request or an external access restriction, then define a confirmed diagnosis or actionable error handling as the outcome.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100