Hi David, I have tried to disable both the NONPARAM and the ACCMASS options. When the NONPARAM option is disabled there is no error massage,only a warning that "Mixture model quality test failed for all the charges, but all the peptides are having a negative prpbability (as I wrote in my first massage). Only when the NONPARAM option is enabled the peptides probabilities are calculated, though the error massage appears. I guess for now, the best option is to use the X!tandem search for the peptide prophet anaysis.
Best regards, Keren On Jun 18, 4:40 pm, David Shteynberg <[email protected]> wrote: > Hi Keren, > > I forgot to mention that the error may also be getting caused by use > of the NONPARAM (semi-parametric modelling option). Please disable > this option for Mascot until the next release is available. Actually, > either the ACCMASS or the NONPARAM could be causing your error > message. Please try to disable the NONPARAM option first and if the > error still comes up disable the ACCMASS too. > > Thanks, > -David > > On Thu, Jun 18, 2009 at 6:38 AM, David > > > > Shteynberg<[email protected]> wrote: > > Hi Keren, > > > You've managed to hit a bug in the current release that's been fixed > > in the upcoming release. To avoid this problem for now and to process > > your dataset you can disable the ACCMASS option which is causing the > > error, until the next release is available. I would also advise that > > you don't use any non-alphanumeric characters in your DECOY tags. '#' > > has a special meaning to some programming languages and may be > > causing this to break. Please try another tag e.g. DECOYXXXX > > > Thanks, > > -David > > > On Wed, Jun 17, 2009 at 11:25 PM, Keren<[email protected]> wrote: > > >> Hello everyone, > > >> I would like to update you regarding my progress with the problem I > >> had. > >> I have reinstalled the apache server and the TPP software. After the > >> reinstalation I have succeeded to get peptide probabilities from > >> peptide prophet with both X!tandem and Mascot searches. Though the > >> peptide analysis with the Mascot search results gave an error massage: > >> "ERROR: NAN probability density detected. Please alert the > >> developer !!!" > >> I have copied the entire command session below. > > >> Keren. > > >> # Commands for session B7GEOBZV7 on Wed Jun 17 09:23:58 2009 > >> # BEGIN COMMAND BLOCK > >> ###### BEGIN Command Execution ###### > >> [Wed Jun 17 09:23:58 2009] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ > >> data/Keren/20172; xinteract -NinteractMascot20172.pep.xml -p0.05 -l7 - > >> OANFP -d### c:/Inetpub/wwwroot/ISB/data/Keren/20172/ > >> Seq20172_Ilan_E2O2.pep.xml > >> OUTPUT: > > >> C:\Inetpub\tpp-bin\xinteract.exe (TPP v4.2 JETSTREAM rev 1, Build > >> 200904071723 (MinGW)) > > >> running: "C:/Inetpub/tpp-bin/InteractParser > >> "interactMascot20172.pep.xml" "c:/Inetpub/wwwroot/ISB/data/Keren/20172/ > >> Seq20172_Ilan_E2O2.pep.xml" -L"7"" > >> file 1: c:/Inetpub/wwwroot/ISB/data/Keren/20172/ > >> Seq20172_Ilan_E2O2.pep.xml > >> processed altogether 7958 results > > >> results written to file c:/Inetpub/wwwroot/ISB/data/Keren/20172/ > >> interactMascot20172.pep.xml > > >> direct your browser > >> tohttp://localhost/ISB/data/Keren/20172/interactMascot20172.pep.shtml > > >> command completed in 4 sec > > >> running: "C:/Inetpub/tpp-bin/PeptideProphetParser > >> "interactMascot20172.pep.xml" MINPROB=0.05 ACCMASS NONTT FORCEDISTR > >> NONPARAM DECOY=###" > >> using Accurate Mass Bins > >> Using Decoy Label "###". > >> Not using ntt model > >> Forcing output of mixture model > >> Using non-parametric distributions > >> (MASCOT) > >> results for charge 1: 4588 id tot and 36 adj scores > >> results for charge 1: -5.94114 adj_ion_mean and 1.49971 adj_ion_hom > >> mean 49.191id mean0.2783 correlation (r) > >> 1+ ion - id = 2.16102*(ion - hom) + -9.18205 with error = 8.34861 > >> mean ion - id: -5.94114, mean ion - hom: 1.49971 > >> adding Accurate Mass mixture distr > >> results for charge 2: 3141 id tot and 46 adj scores > >> results for charge 2: -6.28644 adj_ion_mean and 6.818 adj_ion_hom mean > >> 49.7178id mean0.721109 correlation (r) > >> 2+ ion - id = 1.03256*(ion - hom) + -13.3264 with error = 6.70693 > >> mean ion - id: -6.28644, mean ion - hom: 6.818 > >> results for charge 3: 185 id tot and 0 adj scores > > >> ...skipping 1475 lines of output... [ view all ] > > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> ERROR: NAN probability density detected. Please alert the > >> developer !!! > >> command completed in 41 sec > > >> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i > >> interactMascot20172.pep.xml" > >> Analyzing interactMascot20172.pep.xml ... > >> Reading Accurate Mass Model model +1 ... > >> Reading Accurate Mass Model model +2 ... > >> Reading Accurate Mass Model model +3 ... > >> Reading Accurate Mass Model model +4 ... > >> Reading Accurate Mass Model model +5 ... > >> Reading Accurate Mass Model model +6 ... > >> Reading Accurate Mass Model model +7 ... > >> Parsing search results "c:/Inetpub/wwwroot/ISB/data/Keren/20172/ > >> Seq20172_Ilan_E2O2 (MASCOT)"... > >> => Total of 3190 hits. > >> command completed in 2 sec > > >> running: "C:/Inetpub/tpp-bin/DatabaseParser > >> "interactMascot20172.pep.xml"" > >> command completed in 0 sec > > >> running: "C:/Inetpub/tpp-bin/RefreshParser > >> "interactMascot20172.pep.xml" "c:/Inetpub/wwwroot/ISB/data/dbase/ > >> uniprot_homo09_decoy_appended.fasta""- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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