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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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