Hi,

I have just updated and compiled the percolator, but it looks like the protein IDs are missing for some identifications. I am using a make-pin.pin file as an input and it contains the Protein ID correctly, but it isn't available in the output. For instance, this is a line in the input:
target_0_7648_2_1 1 7648 1965.0727 1965.0654 0.69314718 0.82280302 0.80805397 4.94423580 2899.40405273 0.78125000 17 0 1 0 1 1 0 7.21081829 0.00363823 0.00363823 R.VQHEVIELTATIDQLQK.D F07A5.7a
The last field is the protein ID, but it is missing from the output:
target_0_7648_2_1 1.95614 0.000699343 6.45072e-06 R.VQHEVIELTATIDQLQK.D

I note that the protein ID is present for most identifications. I also observe the same in the PSMs output and in the peptide output files.
Am I doing something wrong or is this a bug in percolator?

I am attaching the input and the output files.
percolator.target.peptides.txt
make-pin.pin.txt

The command line I used:
~/percolator --results-peptides tide-xcorr/percolator.target.peptides.txt --decoy-results-peptides tide-xcorr/percolator.decoy.peptides.txt --results-psms tide-xcorr/percolator.target.psms.txt --decoy-results-psms tide-xcorr/percolator.decoy.psms.txt make-pin.pin

Thanks a lot!