sokrypton / sokrypton/ColabFold
Unknown Error in this Book (ColabFold v1.5.5: AlphaFold2 w/ MMseqs2 BATCH)
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- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
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Description
Dear ColabFold team,
I encountered this issue just 2 hours ago whilst trying to start another batch of prediction using this program.
It was working well just last night and was able to predict ~40 structures before the run ended due to maxed GPU RAM overtime.
Installation step worked fine when the error occured. The, once I click run prediction it gives that error.
When I then try to reinstall, the 2nd error appeared:
Any ideas on how to fix and work around this?
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 reproducing the ColabFold v1.5.5 AlphaFold2 with MMseqs2 batch prediction failure described in the issue, then investigate the separate error that appears during reinstallation. Use the attached screenshots and the reported sequence of a previously successful run, GPU-memory exhaustion, and a later failed run to define the failure conditions; done means identifying a reproducible cause and documenting a verified workaround or fix.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100