sokrypton / sokrypton/ColabFold

MSA server stuck in pending forever?

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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
)

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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

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