The relevant line is "=> Total of 0 hits." Take a look at the interact.pep.xml file and see if there really are any results with >0.05 probability values. It's possible that while the search did complete without error, the input comes from a bad sample, or the search parameters may not be set correctly (wrong database used, etc).
Natalie On Fri, Oct 2, 2009 at 12:29 AM, Tabo <[email protected]> wrote: > > Hi there, > we recently installed TPP (v4.3 JETSTREAM rev 1, Build 200909091257 > (MinGW)) on a Windows XP (SP2 machine). The data we're analysing is > generated on an ABI/SCIEX QStar, which we've converted into mzXML > using mzwiff. > > The mzXML data converts fine in TPP (using the Tandem analysis > pipeline) and the database search works fine on the resulting *.tandem > file. We're able to convert these files into *.pepXML format and view > them in the PepXML Viewer without any problem. > > We're unable however to analyse the *.pepXML data using XInteract. > We'd like to run PeptideProphet then ProteinProphet, but each time we > do the following error is generated: > > ******************************************************************************************************************** > run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\xinteract - > Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/wwwroot/ISB/data/ > 6hrs_Control_Dupl1-s1.tandem.pep.xml > -------------------------------------------------------------------------------- > > *********** > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build > 200909091257 (MinGW)) > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ > Inetpub/wwwroot/ISB/data/6hrs_Control_Dupl1-s1.tandem.pep.xml" -L"7"" > file 1: c:/Inetpub/wwwroot/ISB/data/6hrs_Control_Dupl1- > s1.tandem.pep.xml > processed altogether 3278 results > > > results written to file c:/Inetpub/wwwroot/ISB/data/interact.pep.xml > > direct your browser to http://localhost/ISB/data/interact.pep.shtml > > > command completed in 1 sec > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.05" > (X! Tandem (k-score)) > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: ABI / SCIEX, Model: unknown, > Ionization: ESI, Analyzer: TOFMS, Detector: unknown > > > -------------------------------------------------------------------------------- > ...skipping 20 lines of output... > -------------------------------------------------------------------------------- > > => Total of 0 hits. > command completed in 0 sec > > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > command completed in 0 sec > > running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "c:/ > Inetpub/wwwroot/ISB/data/PfalciparumAnnotatedProteins61.fasta"" > - Searching the tree... > - Linking duplicate entries... - Printing results... > > - Building Commentz-Walter keyword tree...command completed in 1 > sec > > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > wwwroot/ISB/data/interact.pep.xml" > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > wwwroot/ISB/data/interact.pep.xml" failed: Unknown error > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > wwwroot/ISB/data/interact.pep.xml" exited with non-zero exit code: > -1073741819 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O > c:/Inetpub/wwwroot/ISB/data/6hrs_Control_Dupl1-s1.tandem.pep.xml" > failed: Unknown error > > ******************************************************************************************************************************* > > Is anyone able to assist in establishing what the problem is, and the > best solution to follow? If need be we can ftp the error files > generated by the command, or an example *.pepXML data file (<4Mb). > > Thanks in advance > > Tabo > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
