Identification input of combined forward decoy search (reindex with PeptideIndexer first) [idXML,opt.]Identification input of forward run [idXML,opt.]Identification input of decoy run [idXML,opt.]Identification output with forward scores converted to probabilities [idXML]The text sent to standard out during the execution of IDDecoyProbability.The text sent to standard error during the execution of IDDecoyProbability. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)