sokrypton / sokrypton/ColabFold
MSA server stuck in pending forever?
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Hello,
I am trying out boltz2 and in the first step it submits a request to the colabfold API to generate an MSA (endpoint ticket/msa). However, whilst some of the jobs have successfully run there's a few sequences that are stuck in PENDING forever (more than a day).
I've digged in the code and it seems that if you send the same request again you get the back the same ID, which goes immediately to PENDING status, which means that restarting the boltz2 job results in failure again.
Is there anything else I can try?
One of the problematic IDs is this:
Ez8z1KGqCpJwQSCrtMDmsb-7kRUP31vF92DQZA
You can check the status by manually sending a POST request:
host_url = "https://api.colabfold.com"
headers["User-Agent"] = "boltz"
res = requests.get(
f"{host_url}/result/download/Ez8z1KGqCpJwQSCrtMDmsb-7kRUP31vF92DQZA", timeout=6.02, headers=headers
)
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 checking the ticket/msa submission and the result/download/Ez8z1KGqCpJwQSCrtMDmsb-7kRUP31vF92DQZA request described in the report. Determine whether the indefinite PENDING state comes from the ColabFold API or from boltz2's handling of the response. Done means identifying a reproducible cause and documenting or implementing a recovery path for affected MSA jobs.
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