id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14775 AlphaFold not running (Invalid character in the sequence) MCINNES@… Tom Goddard "{{{ 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] 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 http://www.sc.edu/pharmacy }}} [[Image(image001.png)]] " defect closed normal Structure Prediction fixed all ChimeraX