Known Issues

  1. Q-Ranker and Barista detect decoy PSMs by use of the --decoy-prefix string (ex. rand_) which is appended to the beginning of the peptide's protein IDs. Currently, running the search-for-matches command with a fasta file generates protein ids from decoy PSMs without the "rand_" prefix. This issue will cause the following error for QRanker and Barista:
        FATAL: Cannot compute PEP without target or decoy scores.
        
    To prevent the error, run the search-for-matches with an index.
  2. The --use-spec-features option in Q-Ranker does not work if the search results contain modified peptides.
  3. In Percolator, a seed value of 0 will produce a segmentation fault, so it is automatically set to 1 instead.