ConsensusID fails with

Dear colleagues,

I have following workflow:

PepideID with MSGFPlus, Comet and XTandem -> IDposteriorErrorProbability ->File merger ->ID Merger -> ConsensusID.

ConsenusID fails with:
“Error: Unexpected internal error (the element 'No accession DECOY_sp|O75369|FLNB_HUMAN found in run ‘’ for PSM KQSLVELLAILR_3.”

Any ideas ?


Can you try it without the IDMerger and activate the new “–per_spectrum” mode
in ConsensusID? That is how I currently use it successfully.
Honestly, we might have broken something with the old mode since we are more strict on 100% valid idXMLs now.

Details: I assume that if you IDFilter ALL proteins (without removing the referenced peptides) before going into ConsensusID, it should work, too. The problem is that the previous ConsensusID mode invalidates associated proteins but does not update the peptide information. And this is not allowed anymore. Seems like our tests for the old mode did not have files with protein information :confused:


Dear Julianus,

thanks for the prompt reply. The per spectrum switch died the trick. Works like a charm !!! Chapeau !!!