Hello Ian, even I am getting the same error, any clue regarding how to solve the problem will be really helpful.
Regards, Rishika On Thursday, 13 November 2008 23:55:55 UTC-5, Ian wrote: > > Hi Natalie and Brain, > It seems I posted a half baked question. > > Here is a fresh TPP run and output, as you will see below Protein > prophet quits even when the peptide output probabilities are above > 0.05: > > [root@localhost output_added]# ../bin/xinteract -p0 -Noutput.xml -Op > pep.xml > > ../bin/xinteract (TPP v4.1 JETSTREAM rev 0, Build 200811111648 > (linux)) > > running: "/var/TPP_new/bin/InteractParser 'output.xml' 'pep.xml' - > L'7'" > file 1: pep.xml > processed altogether 7850 results > > results written to file /var/TPP_new/output_added/output.shtml > > command completed in 3 sec > > running: "/var/TPP_new/bin/PeptideProphetParser 'output.xml' > MINPROB=0" > (X! Tandem (k-score)) (minprob 0) > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: ThermoFinnigan, Model: LCQ Deca XP, > Ionization: ESI, Analyzer: Ion Trap, Detector: EMT > > PeptideProphet (TPP v4.1 JETSTREAM rev 0, Build 200811111648 (linux)) > AKeller@ISB > read in 504 1+, 3602 2+, 3610 3+, 0 4+, and 0 5+ spectra > Initialising statistical models ... > negmean = -0.551996 > negmean = -2.05583 > negmean = -1.56374 > negmean = -0.2 > negmean = -0.2 > Iterations: .........10.........20....... > model complete after 28 iterations > command completed in 3 sec > > running: "/var/TPP_new/bin/ProphetModels.pl -i output.xml" > Analyzing output.xml ... > Parsing search results "/var/TPP_new/input_added/7MIX_STD_110802_1 (X! > Tandem (k-score))"... > => Total of 7716 hits. > Can't exec "gnuplot": No such file or directory at /var/TPP_new/bin/ > ProphetModels.pl line 376. > command completed in 0 sec > > running: "/var/TPP_new/bin/DatabaseParser 'output.xml'" > command completed in 0 sec > > running: "/var/TPP_new/bin/RefreshParser 'output.xml' '/var/TPP_new/ > fasta/crap.fasta.pro'" > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > > command completed in 2 sec > > running: "/var/TPP_new/cgi-bin/PepXMLViewer.cgi -I /var/TPP_new/ > output_added/output.xml" > command completed in 2 sec > > running: "/var/TPP_new/bin/ProteinProphet 'output.xml' > 'output.prot.xml' XML" > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > original Perl by A. Keller (TPP v4.1 JETSTREAM rev 0, Build > 200811111648 (linux)) > (xml input) (using degen pep info) > . . . reading in /var/TPP_new/output_added/output.xml. . . > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+ spectra with min prob 0.05 > no data - quitting > > Ian > > > Natalie Tasman wrote: > > Hello Ian, > > > > I'm not sure what's going on with ProteinProphet, but if you're running > > xinteract on the commandline, you'll need to at least specify the "-Op" > > option to run ProteinProphet as well. > > > > Natalie > > > > On Thu, Nov 13, 2008 at 8:57 AM, Ian <[email protected] <javascript:>> > wrote: > > > > > > > > Hi All, > > > I am trying to give a dry run with TPP using the > > > "7MIX_STD_110802_1.xml' file available at > > > http://sashimi.sourceforge.net/repository.html > > > > > > All modules expect Protein Prophet work fine. It generates the > > > following error: > > > > > > C:\Inetpub\tpp-bin>ProteinProphet.exe put2.xml outout > > > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the > > > original Pe > > > rl by A. Keller (TPP v4.1 JETSTREAM rev 0, Build 200811101627 (MinGW)) > > > (xml input) (using degen pep info) > > > . . . reading in C:/Inetpub/tpp-bin/put2.xml. . . > > > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+ spectra with min prob 0.05 > > > no data - quitting > > > > > > I have verified the peptide prophet output file put2.xml, it has a > > > number of hits with probability >0.05. > > > Any tips how to fix this issue? > > > > > > Also when I try running xinteract command, it does not invoke Protein > > > Prophet ...stops after peptide prophet. I was able to generate these > > > errors on Fedora 8 also. > > > > > > Regards, > > > Ian > > > > > > > > > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
