Known Issues
- 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 thesearch-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.- The
--use-spec-features
option in Q-Ranker does not work if the search results contain modified peptides.- In Percolator, a seed value of 0 will produce a segmentation fault, so it is automatically set to 1 instead.