Jennifer,

It looks like Protein Prophet is not finding any Proteins that match your search criteria. And it thus is erroring out with an error code of 256.

I have cut and pasted the pertinent lines from the log file that you sent.

26 Jan 2012 20:23:02,711 INFO : running: "ProteinProphet 'beiRa.pep.xml' 'beiRa.prot.xml' XML NOPLOT"
26 Jan 2012 20:23:02,740 INFO : ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 201002051140 (linux))
26 Jan 2012 20:23:02,751 INFO : (xml input) (report Protein Length) (using degen pep info)
26 Jan 2012 20:23:02,775 INFO : . . . reading in /tmp/17651.1.labkey/beiRa59520.work/beiRa.pep.xml. . .
26 Jan 2012 20:23:02,776 INFO : . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05
26 Jan 2012 20:23:02,778 INFO : no data - quitting
26 Jan 2012 20:23:02,783 INFO : command "ProteinProphet 'beiRa.pep.xml' 'beiRa.prot.xml' XML NOPLOT" exited with non-zero exit code: 256
26 Jan 2012 20:23:02,785 INFO : QUIT - the job is incomplete
26 Jan 2012 20:23:02,787 INFO : Failed to complete task 'org.labkey.ms2.pipeline.TPPTask'
26 Jan 2012 20:23:02,792 ERROR: Failed to remove work directory /tmp/17651.1.labkey/beiRa59520.work unexpected files found:

This is causing the search to fail.

-Brian

Thanks a lot Brian.