Thanks Kshitiz, actually that's what I was guessing. The problem might occur during x!tandem results loading into the xinteract, somehow it did not pick up the tandem results properly. I did used a target-reverse concatenated database and used a quite loose searching parameter, which gives a lot of decoy hits. But just by looking at the pepXML itself, the target hits (BSA only actually) still single out pretty nicely with very low x!tandem expect score.
SunSun On Tue, Jul 31, 2012 at 3:20 PM, kshitiz <[email protected]> wrote: > Hi, > I am not an expert but I can try to give some clues. Also I work on the > linux version. > > Your prophet models failed for charge 3+. This is not good and I have > never seen this with my data. Do you have a decoy database concatenated and > randomised in the database that you used to search with X!Tandem? If yes > then are you passing the right parameters in the xinteract command? > > The error with PepXMLViewer.cgi is not due to a problem with with the > viewer itself but it suggests there was a problem upstream of the viewer > and it is complaining because there is no data for it to process. I have > seen this one before and it happens when there is no high quality data from > the mass spec runs. Try may be changing the default tolerance on your > xinteract. > > Hope it helps, > Cheers, > Kshitiz Tyagi > > > On Tuesday, July 31, 2012 12:33:37 AM UTC+1, sunsun wrote: >> >> >> Dear TPP team: >> I came across a error message that I really cannot explain why. Hopefully >> some of experts here can help me to decode the message. Really appreciated! >> The data was collected from a LTQ-Orbitrap, the search was done by X!tandem >> within the TPP environment using the default setting >> "isb_default_input_kscore setting". >> >> The search result was automatically converted to pep.xml and when I try to >> filter the results with peptideprophet I got error message like this: >> ______________________________**______________________________**______________________________**______________________________**_____ >> >> run_in c:/Inetpub/wwwroot/ISB/data/**data/AIF/20120728/processed; >> c:\Inetpub\tpp-bin\xinteract -Nbsa1_3con_filtered.pep.xml -p0.95 -l7 -O >> bsa1_3con.tandem.pep.xml >> >> ------------------------------ >> >> c:\Inetpub\tpp-bin\xinteract (TPP v4.5 RAPTURE rev 2, Build 201202031108 >> (MinGW)) >> >> running: "C:/Inetpub/tpp-bin/**InteractParser "bsa1_3con_filtered.pep.xml" >> "bsa1_3con.tandem.pep.xml" -L"7"" >> file 1: bsa1_3con.tandem.pep.xml >> processed altogether 4615 results >> >> >> results written to file >> c:/Inetpub/wwwroot/ISB/data/**data/AIF/20120728/processed/**bsa1_3con_filtered.pep.xml >> >> direct your browser to >> http://localhost/ISB/data/**data/AIF/20120728/processed/**bsa1_3con_filtered.pep.shtml >> >> <http://localhost/ISB/data/data/AIF/20120728/processed/bsa1_3con_filtered.pep.shtml> >> >> >> >> command completed in 1 sec >> >> running: "C:/Inetpub/tpp-bin/**DatabaseParser "bsa1_3con_filtered.pep.xml"" >> command completed in 1 sec >> >> running: "C:/Inetpub/tpp-bin/**RefreshParser "bsa1_3con_filtered.pep.xml" >> "c:/Inetpub/wwwroot/ISB/data/**dbase/BOVIN_DECOY.fasta"" >> >> >> ------------------------------ >> * ...skipping 23 lines of output... * >> ------------------------------ >> >> WARNING: Mixture model quality test failed for charge (3+). >> model complete after 25 iterations >> command completed in 1 sec >> >> running: "C:/Inetpub/tpp-bin/**ProphetModels.pl -i >> bsa1_3con_filtered.pep.xml" >> Analyzing bsa1_3con_filtered.pep.xml ... >> Parsing search results >> "c:/Inetpub/wwwroot/ISB/data/**data/AIF/20120728/processed/**bsa1_3con (X! >> Tandem (k-score))"... >> => Total of 0 hits. >> => Total of 0 decoy hits. >> => Total of 0 excluded hits. >> command completed in 0 sec >> >> running: "c:/Inetpub/wwwroot/../tpp-**bin/PepXMLViewer.cgi -I >> c:/Inetpub/wwwroot/ISB/data/**data/AIF/20120728/processed/**bsa1_3con_filtered.pep.xml" >> >> command "c:/Inetpub/wwwroot/../tpp-**bin/PepXMLViewer.cgi -I >> c:/Inetpub/wwwroot/ISB/data/**data/AIF/20120728/processed/**bsa1_3con_filtered.pep.xml" >> failed: Unknown error >> >> command "c:/Inetpub/wwwroot/../tpp-**bin/PepXMLViewer.cgi -I >> c:/Inetpub/wwwroot/ISB/data/**data/AIF/20120728/processed/**bsa1_3con_filtered.pep.xml" >> exited with non-zero exit code: 255 >> QUIT - the job is incomplete >> >> command "c:\Inetpub\tpp-bin\xinteract -Nbsa1_3con_filtered.pep.xml -p0.95 >> -l7 -O bsa1_3con.tandem.pep.xml" failed: Unknown error >> >> *Command FAILED >> __________________________________________________________ >> >> thank you so much in advance! >> >> sunsun >> * >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/06bIisXYpqMJ. > > 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. > -- 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.
