sokrypton / sokrypton/ColabFold
Encountering Rate Limit Despite MSA Server Not Being Used
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Description
Expected Behavior
I expect structures to be predicted without a rate limit.
Current Behavior
I have provided .a3m files already with the expectation I can avoid connecting to the server and getting a rate limit.
This seems to work fine for the first 25 sequences and then I am provided a rate limit again of ~ 90 seconds between structures.
Steps to Reproduce (for bugs)
colabfold_batch --num-recycle 0 --num-models 1 fasta_file.fasta output_dir_with_a3m_files
ColabFold Output (for bugs)
2025-01-13 14:33:42,599 Sleeping for 8s. Reason: RATELIMIT... etc.
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
Start by running the reported colabfold_batch command with the supplied .a3m files and trace why it still reaches the rate-limit path after the first 25 sequences. Done means locally supplied alignments no longer trigger the reported ~90-second delay, with the behavior verified for this reproduction.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100