AlphaFold not running (Invalid character in the sequence)

[MCINNES@…]

Please see below. AlphaFold has stopped working for some reason and I get the following:


2024-03-15 15:04:57,761 Starting prediction on 2024-03-15 UTC time
2024-03-15 15:04:57,762 Installing ColabFold on Google Colab virtual machine.
Using Tesla T4 graphics processor
2024-03-15 15:04:57,986 Running on GPU
2024-03-15 15:04:57,990 Found 5 citations for tools or databases
2024-03-15 15:04:57,990 Query 1/1: af42 (length 42)
COMPLETE: 100%|██████████| 150/150 [elapsed: 00:01 remaining: 00:00]
2024-03-15 15:04:59,631 Could not generate input features af42: Invalid character in the sequence:
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/colabfold/batch.py", line 1512, in run
    = generate_input_feature(query_seqs_unique, query_seqs_cardinality, unpaired_msa, paired_msa,
  File "/usr/local/lib/python3.10/dist-packages/colabfold/batch.py", line 1039, in generate_input_feature
    feature_dict = build_monomer_feature(
  File "/usr/local/lib/python3.10/dist-packages/colabfold/batch.py", line 892, in build_monomer_feature
    **pipeline.make_sequence_features(
  File "/usr/local/lib/python3.10/dist-packages/alphafold/data/pipeline.py", line 40, in make_sequence_features
    features['aatype'] = residue_constants.sequence_to_onehot(
  File "/usr/local/lib/python3.10/dist-packages/alphafold/common/residue_constants.py", line 580, in sequence_to_onehot
    raise ValueError(f'Invalid character in the sequence: {aa_type}')
ValueError: Invalid character in the sequence:
2024-03-15 15:04:59,633 Done
Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold
cp: cannot stat '*_relaxed_rank_001_*.pdb': No such file or directory

cp: cannot stat '*_scores_rank_001_*.json': No such file or directory






[Macintosh HD:Users:aerius:Downloads:FW__Pharmacy_logos:Pharmacy_Standard_202.eps]<http://www.sc.edu/pharmacy>
Campbell McInnes, Ph.D.
Professor, Medicinal Chemistry
Drug Discovery and Biomedical Sciences

University of South Carolina
College of Pharmacy
CLS 717A
715 Sumter Street
Columbia, South Carolina

803.576.5684 (o)
803.338.6340 (c)
mcinnes@cop.sc.edu<mailto:mcinnes@cop.sc.edu>
http://www.sc.edu/pharmacy

[MCINNES@…]

Added by email2trac

[Eric Pettersen]

Reported by Campbell McInnes

[Tom Goddard]

ChimeraX Alphafold prediction is broken due to a change in Google Colab. I am not sure when it will get fixed, may be days or maybe in April when I am back from vacation. The problem is sending the sequence to Google Colab no longer works. I don't see any simple fix.

[Tom Goddard]

Fixed in the daily build.

More details in ticket #14777.