sokrypton / sokrypton/ColabFold
prediction fail for a specific sequence
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Description
Expected Behavior
Current Behavior
A specific sequence fails on local or google colab latest version of ColabFold.
Steps to Reproduce (for bugs)
Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
Please use the sequence from Uniprot Q3L181, 'MPRVKLGTQGLEVSKLGFGCMGLSGDYNDALPEEQGIAVIKEAFNCGITFFDTSDIYGENGSNEELLGKALKQLPREKIQVGTKFGIHEIGFSGVKAKGTPDYVRSCCEASLKRLDVDYIDLFYIHRIDTTVPIEITMGELKKLVEEGKIKYVGLSEASPDTIRRAHAVHPVTALQIEYSLWTRDIEDEIVPLCRQLGIGIVPYSPIGRGLFAGKAIKESLPENSVLTSHPRFVGENLEKNKQIYYRIEALSQKHGCTPVQLALAWVLHQGEDVVPIPGTTKIKNLHNNVGALKVKLTKEDLKEISDAVPLDEVAGESIHEVIAVTNWKFANTPPLK'.
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Downloading alphafold2 weights to .: 100%|██████████| 3.47G/3.47G [00:25<00:00, 144MB/s]
2023-05-24 15:28:06,480 Running on GPU
2023-05-24 15:28:06,890 Found 5 citations for tools or databases
2023-05-24 15:28:06,891 Query 1/1: Q3L181_8c443 (length 337)
COMPLETE: 100%|██████████| 150/150 [elapsed: 00:02 remaining: 00:00]
2023-05-24 15:28:13,664 Setting max_seq=512, max_extra_seq=5120
2023-05-24 15:29:18,365 Could not predict Q3L181_8c443. Not Enough GPU memory? INTERNAL: cublas error
2023-05-24 15:29:18,367 Done
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used
- If you run it on a local system. Please add the server specifications
- Operating system and version:
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 Q3L181 sequence with colabfold_batch after a Colab factory reset or local update. Inspect the reported cublas error alongside the available GPU memory and the complete environment details. Done means identifying a reproducible cause and documenting a confirmed fix or workaround for this prediction failure.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100