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<keren.benda...@gmail.com> 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 to > http://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"" > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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