sokrypton / sokrypton/ColabFold
MSA requests remain in PENDING state (ColabFold server, Boltz2)
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Description
Dear ColabFold team,
I am running a Boltz2 pipeline that relies on the ColabFold MSA server. For a subset of input sequences (provided via a .txt file), the MSA requests remain indefinitely in the PENDING state and do not progress to RUNNING or completion.
Other 90% sequences that I worked with have been processed successfully, but the affected ones consistently stall even after repeated attempts. I have also retried multiple times with pauses between submissions, but the issue persists.
Could you please advise whether this is a known issue or if there are recommended ways to handle such stalled requests?
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 with the attached failed_sequences.txt and reproduce the ColabFold MSA server requests for those sequences, comparing them with the 90% that completed successfully. Investigate why the affected requests remain PENDING rather than reaching RUNNING or completion; done means identifying a reproducible cause or documented handling for the stalled requests.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100