Invalid percentile rank epitopes

[rschenck]

Error received:

Traceback (most recent call last):
  File "/Users/Ryan/anaconda2/bin/topiary", line 64, in <module>
    main()
  File "/Users/Ryan/anaconda2/bin/topiary", line 46, in main
    epitopes = predict_epitopes_from_args(args)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/topiary/predict_epitopes.py", line 296, in predict_epitopes_from_args
    raise_on_variant_effect_error=not args.skip_variant_errors)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/topiary/predict_epitopes.py", line 263, in predict_epitopes_from_variants
    wildtype_ligandome_dict=wildtype_ligandome_dict)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/topiary/predict_epitopes.py", line 159, in predict_epitopes_from_mutation_effects
    binding_predictions = mhc_model.predict(protein_subsequences)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/mhctools/base_commandline_predictor.py", line 276, in predict
    prediction_method_name=self.program_name)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/mhctools/file_formats.py", line 249, in parse_netmhciipan_stdout
    contains_class2_columns=True)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/mhctools/file_formats.py", line 236, in parse_netmhcpan_stdout
    log_ic50=log_affinity)
  File "/Users/Ryan/anaconda2/lib/python2.7/site-packages/mhctools/epitope_collection_builder.py", line 96, in add_binding_prediction
    rank, peptide, allele))
ValueError: Invalid percentile rank 14631.83 for QRASPRAPAPC w/ allele DRB1_0101``

When running topiary as follows: $ topiary --vcf test.vcf --mhc-predictor netmhciipan --mhc-alleles DRB1*01:23 --output-csv epitope_test.csv --skip-variant-errors --reference-name grch37

Things I have tried:

1. Running the script with and without --skip-variant-errors option. This didn't change anything.
2. Changing the allele selected for netmhciipan (the local install appears to be working fine)
3. Running the script with a different genome assembly (GRCH38; couldn't get it to work with Ensembl release 74; only release 75

I went so far as to find the portion of code raising this error and I put a pass in place of the error just to see what would happen (Line 96 of epitope_collection_builder.py). The process finished, but I receive %rank values ranging from 11.56 to 43258.78. Any help would be appreciated.

-Ryan

[iskandr]

Hey @rschenck, sorry for the trouble. The Class II epitope prediction is definitely the least used/tested part of Topiary so I guess I'm not surprised something is wonky there. Can you paste the variant which is causing this error (or email it to me if don't want it on github)?

[rschenck]

Sending you an email now. Thanks.

[iskandr]

@tavinathanson Just a reminder for both of us that we should fix this soon.

[tavinathanson]

Looks like this is an issue with NetMHCIIpan 3.0 output vs 3.1 output; we should (at the least) be more clear about which versions we support, and (better yet) support 3.1 soon.

[rschenck]

Thanks for the help gentlemen.