SchemaEvaluator: alignment file missing raising error

[domenico-simone]

Hello,

while using the SchemaEvaluator module, I got the following error:

Traceback (most recent call last):
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/bin/chewBBACA.py", line 8, in <module>
    sys.exit(main())
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/CHEWBBACA/chewBBACA.py", line 1414, in main
    functions_info[process][1]()
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/CHEWBBACA/utils/process_datetime.py", line 149, in wrapper
    func(*args, **kwargs)
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/CHEWBBACA/chewBBACA.py", line 597, in evaluate_schema
    input_files, pre_computed_data_path, protein_file_path, output_file, minimum_length, chewie_schema=True)
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/CHEWBBACA/SchemaEvaluator/schema_evaluator.py", line 1269, in write_individual_html
    msa_seq_gen = SeqIO.parse(msa_file_path, "fasta")
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line 607, in parse
    return iterator_generator(handle)
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
    super().__init__(source, mode="t", fmt="Fasta")
  File "/lustrehome/dsimone/miniconda3/envs/chewbbaca/lib/python3.6/site-packages/Bio/SeqIO/Interfaces.py", line 47, in __init__
    self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: 'SchemaEvaluator/SchemaEvaluator_pre_computed_data/prot_files/genome1-protein1171_aligned.fasta'

I checked the file genome1-protein1171.fasta and turns out it has only one sequence, therefore my hypothesis is that the alignment file was not generated. Is there any way I can overcome this issue?

Thank you

Domenico

[rfm-targa]

Greetings @domenico-simone,

Thank you for your interest in chewBBACA and sorry for the delayed response. It does seem like the process is failing because it was not possible to generate the file with the MSA. We solved some issues related with loci that had a single allele, but this might be a similar issue that we still need to patch. Can you send us the Fasta file for the locus that is leading to this issue? It would help us to quickly identify the cause. Without a bugfix, the only way to avoid this is to remove that locus from the schema.

Best regards,

Rafael

[ramirma]

Following up on @rfm-targa's response you can use our general email imm-bioinfo[at]medicina.ulisboa.pt if you would like to send it privately.