issues with uniprot.fasta file integrity when returning jackhmmer results

[avilella]

Similar to bug #465 , I also get issues like the one below:

I0516 08:33:11.303210 140061298210624 jackhmmer.py:133] Launching subprocess "/home/user/miniconda3/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpx9qnk8ys/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -
N 1 /tmp/tmpxejxmx66.fasta /data/quick_share/alphafold2/db_v2.2.0/uniprot/uniprot.fasta"                                                                                                                                                                    
I0516 08:33:11.339200 140061298210624 utils.py:36] Started Jackhmmer (uniprot.fasta) query                                                                                                                                                                  
I0516 08:35:12.610642 140061298210624 utils.py:40] Finished Jackhmmer (uniprot.fasta) query in 121.271 seconds                                                                                                                                              
Traceback (most recent call last):                                                                                                                                                                                                                          
  File "/home/user/alphafold-2.2.0/run_alphafold.py", line 422, in <module>                                                                                                                                                                             
    app.run(main)                                                                                                                                                                                                                                           
  File "/home/user/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run                                                                                                                                                 
    _run_main(main, args)                                                                                                                                                                                                                                   
  File "/home/user/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main                                                                                                                                           
    sys.exit(main(argv))                                                                                                      
  File "/home/user/alphafold-2.2.0/run_alphafold.py", line 398, in main                                                                                                                                                                                 
    predict_structure(                                                                                                        
  File "/home/user/alphafold-2.2.0/run_alphafold.py", line 172, in predict_structure                                      
    feature_dict = data_pipeline.process(                                                                                                                                                                                                                   
  File "/home/user/alphafold-2.2.0/alphafold/data/pipeline_multimer.py", line 264, in process                                                                                                                                                           
    chain_features = self._process_single_chain(                                                                                                                                                                                                            
  File "/home/user/alphafold-2.2.0/alphafold/data/pipeline_multimer.py", line 219, in _process_single_chain                                                                                                                                             
    all_seq_msa_features = self._all_seq_msa_features(chain_fasta_path,                                                                                                                                                                                     
  File "/home/user/alphafold-2.2.0/alphafold/data/pipeline_multimer.py", line 227, in _all_seq_msa_features                                                                                                                                             
    result = pipeline.run_msa_tool(                                                                                                                                                                                                                         
  File "/home/user/alphafold-2.2.0/alphafold/data/pipeline.py", line 96, in run_msa_tool                                                                                                                                                                
    result = msa_runner.query(input_fasta_path)[0]                                                                                                                                                                                                          
  File "/home/user/alphafold-2.2.0/alphafold/data/tools/jackhmmer.py", line 171, in query                                                                                                                                                               
    single_chunk_result = self._query_chunk(                                                                                                                                                                                                                
  File "/home/user/alphafold-2.2.0/alphafold/data/tools/jackhmmer.py", line 142, in _query_chunk                                                                                                                                                        
    raise RuntimeError(                                                                                                                                                                                                                                     
RuntimeError: Jackhmmer failed                                                                                                                                                                                                                              
stderr:                                                                                                                       
                                                                                                                              
Error: Parse failed (sequence file /data/quick_share/alphafold2/db_v2.2.0/uniprot/uniprot.fasta):                                                                                                                                                           
Line 484402440: illegal character 

I tried tinkering with the code a bit and trying to ignore hits that contain these issues, but at the moment I can't find a clean way to do it (this is done as multiprocessing Pool calls that then turn into an array, the elements of which can't be None).

[shahryary]

@avilella check line 484402440, probably you have '*' character in the sequence fasta file.