sokrypton / sokrypton/ColabFold

Exception: MMseqs2 API is giving errors.

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Description

Expected Behavior

Colabfold outputs 5 models.

Current Behavior

Error in the Run Prediction cell

Steps to Reproduce (for bugs)

query sequence: "GAGAGAGAGAGAGAGAGAGAGAGAGAGAGA"

ColabFold Output (for bugs)

2023-10-17 10:51:18,684 Running on GPU
2023-10-17 10:51:18,687 Found 4 citations for tools or databases
2023-10-17 10:51:18,688 Query 1/1: TESTgaga_f5906 (length 30)
PENDING: 0%| | 0/150 [elapsed: 00:00 remaining: ?]
2023-10-17 10:51:19,292 Sleeping for 9s. Reason: PENDING
ERROR: 0%| | 0/150 [elapsed: 00:10 remaining: ?]
2023-10-17 10:51:28,948 Could not get MSA/templates for TESTgaga_f5906: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.
Traceback (most recent call last):
File "/content/colabfold/batch.py", line 1384, in run
= get_msa_and_templates(jobname, query_sequence, a3m_lines, result_dir, msa_mode, use_templates,
File "/content/colabfold/batch.py", line 820, in get_msa_and_templates
a3m_lines = run_mmseqs2(
File "/content/colabfold/colabfold.py", line 238, in run_mmseqs2
raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
Exception: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.
2023-10-17 10:51:28,948 Done

Context

This error persists both using the Colab Notebook and using the local colabfold_batch.
Is the only peptide sequence from a varied and vast list that results in this error.

Your Environment

Include as many relevant details about the environment you experienced the bug in.
NOTEBOOK

  • ColabFold v1.5.2-patch: AlphaFold2 using MMseqs2
    LOCAL
  • Operating system and version: Ubuntu 16.04.7 LTS; Cuda compilation tools, release 11.0, V11.0.167

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 with the Run Prediction path in colabfold/batch.py, especially get_msa_and_templates, and then inspect run_mmseqs2 in colabfold/colabfold.py using the reported peptide sequence. Compare the notebook and local colabfold_batch behavior and determine why this sequence receives the MMseqs2 API error. Done means the cause is identified and the reported sequence is handled or the failure is clearly explained.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, ubuntu
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
32/100

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