sokrypton / sokrypton/ColabFold
ConnectTimeoutError to api.colabfold.com when using Boltz --use_msa_server
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Description
Description:
I am running Boltz2 on an Ubuntu server and using:
boltz predict input.yaml --use_msa_server --use_potentials --accelerator gpu --devices 1 --no_kernels
Boltz fails during MSA generation when it tries to contact the default ColabFold MSA API:
The error is a connection timeout before the MSA job is submitted/completed.
Boltz source/default behavior:
--use_msa_server uses:
https://api.colabfold.com
In the installed Boltz source, requests to the MSA server use a short timeout:
timeout=6.02
with retries.
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 locating the implementation behind --use_msa_server and its timeout=6.02 setting, then reproduce the reported command against https://api.colabfold.com on Ubuntu. Done should mean MSA generation no longer fails from the reported connection timeout, with the behavior verified through the relevant existing checks.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- ubuntu
- Domain
- bioinformatics, networking
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100