key error

[xuewuzhang-UTSW]

Hi Kiarash, I got the following error when trying to run the program with a simple map and sequence file("model_angelo build -v PostProcess/job099/postprocess_masked.mrc -f hS.fasta -o model_angelo/"):

2022-12-01 at 13:13:10 | ERROR | Error in ModelAngelo Traceback (most recent call last):

File "/home/xuewuzhang/miniconda3/envs/model_angelo/bin/model_angelo", line 33, in sys.exit(load_entry_point('model-angelo==0.2.2', 'console_scripts', 'model_angelo')()) \u2502 \u2502 \u2514 <function importlib_load_entry_point at 0x7f4d69444160> \u2502 \u2514 \u2514 <module 'sys' (built-in)> File "/home/xuewuzhang/miniconda3/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.2-py3.9.egg/model_angelo/main.py", line 51, in main args.func(args) \u2502 \u2502 \u2514 Namespace(volume_path='PostProcess/job099/postprocess_masked.mrc', fasta_path='./hS.fasta', output_dir='model_angelo', ma... \u2502 \u2514 <function main at 0x7f4c36565940> \u2514 Namespace(volume_path='PostProcess/job099/postprocess_masked.mrc', fasta_path='./hS.fasta', output_dir='model_angelo', ma...

File "/home/xuewuzhang/miniconda3/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.2-py3.9.egg/model_angelo/apps/build.py", line 225, in main gnn_output = gnn_infer(gnn_infer_args) \u2502 \u2514 {'num_rounds': 3, 'crop_length': 200, 'repeat_per_residue': 3, 'esm_model': 'esm1b_t33_650M_UR50S', 'aggressive_pruning': Tru... \u2514 <function infer at 0x7f4c365658b0> File "/home/xuewuzhang/miniconda3/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.2-py3.9.egg/model_angelo/gnn/inference.py", line 243, in infer protein = get_lm_embeddings_for_protein(lang_model, batch_converter, protein) \u2502 \u2502 \u2502 \u2514 Protein(atom_positions=None, atom14_positions=None, aatype=None, atom_mask=None, atom14_mask=None, residueindex=None, chain... \u2502 \u2502 \u2514 <esm.data.BatchConverter object at 0x7f4c206bd070> \u2502 \u2514 ProteinBertModel( \u2502 (embed_tokens): Embedding(33, 1280, padding_idx=1) \u2502 (layers): ModuleList( \u2502 (0): TransformerLayer( \u2502 ... \u2514 <function get_lm_embeddings_for_protein at 0x7f4c372daca0> File "/home/xuewuzhang/miniconda3/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.2-py3.9.egg/model_angelo/data/generate_complete_prot_files.py", line 32, in get_lm_embeddings_for_protein [result[s]["representations"][33].cpu().numpy() for s in seq_names], \u2502 \u2514 ['0'] \u2514 {} File "/home/xuewuzhang/miniconda3/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.2-py3.9.egg/model_angelo/data/generate_complete_prot_files.py", line 32, in [result[s]["representations"][33].cpu().numpy() for s in seq_names], \u2502 \u2502 \u2514 '0' \u2502 \u2514 '0' \u2514 {}

KeyError: '0'

I am not sure whether my installation was corrupt, or there is a bug in the package. Can you please help? Thanks, Xuewu

[jamaliki]

Hi Xuewu,

This indicates there is something perhaps off about your FASTA file. Could you share this file here? Alternatively, if you are more comfortable you could email it to me.

[jamaliki]

This was an issue with FASTA formatting