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. 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 -~----------~----~----~----~------~----~------~--~---
