Hi all, hoping someone can help me find a solution to this, when analyzing SpectraST resuslts using peptide prophet I wind up with the following error:
The files are direct pepXML output from SpectraST so I haven't played around with them at all. Does anyone have any ideas? Glad for any help. /Erik The complete XInteract output can be seen below.: c:\Inetpub\tpp-bin\xinteract.exe -Einteract -p0.05 -l7 -eT -Op fe_ecoli_mix1_081016_01.pepxml fe_ecoli_mix2_081016_01.pepxml -Ninteract.pep.xml c:\Inetpub\tpp-bin\xinteract.exe (TPP v4.5 RAPTURE rev 1, Build 201111141620 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "C:\inetpub\wwwroot\tmp \1ecece635e644dd3bd110482e8be5f68\interact.pep.xml" "c:\inetpub\wwwroot \isb\data\APP\taskController \Ecolitest40177ed3cd9640da88fd867df9f85129\SpectraSTPlugin \a97498401c0046dda15d1edf86efb7ab\output \fe_ecoli_mix1_081016_01.pepxml" "c:\inetpub\wwwroot\isb\data\APP \taskController \Ecolitest40177ed3cd9640da88fd867df9f85129\SpectraSTPlugin \a97498401c0046dda15d1edf86efb7ab\output \fe_ecoli_mix2_081016_01.pepxml" -X"interact" -L"7" -E"trypsin"" file 1: c:\inetpub\wwwroot\isb\data\APP\taskController \Ecolitest40177ed3cd9640da88fd867df9f85129\SpectraSTPlugin \a97498401c0046dda15d1edf86efb7ab\output \fe_ecoli_mix1_081016_01.pepxml file 2: c:\inetpub\wwwroot\isb\data\APP\taskController \Ecolitest40177ed3cd9640da88fd867df9f85129\SpectraSTPlugin \a97498401c0046dda15d1edf86efb7ab\output \fe_ecoli_mix2_081016_01.pepxml processed altogether 253 results results written to file c:/inetpub/wwwroot/tmp/ 1ecece635e644dd3bd110482e8be5f68/interact.pep.xml direct your browser to http://localhost/tmp/1ecece635e644dd3bd110482e8be5f68/interact.pep.shtml command completed in 0 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "C:\inetpub\wwwroot\tmp \1ecece635e644dd3bd110482e8be5f68\interact.pep.xml"" command completed in 0 sec running: "C:/Inetpub/tpp-bin/RefreshParser "C:\inetpub\wwwroot\tmp \1ecece635e644dd3bd110482e8be5f68\interact.pep.xml" "C:\Inetpub\wwwroot \ISB\data\dbase\uniproteE.coli.reviewed_DECOY_DCYisPrefix.fasta"" - Searching the tree... - Linking duplicate entries... - Printing results... - Building Commentz-Walter keyword tree...command completed in 1 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "C:\inetpub\wwwroot \tmp\1ecece635e644dd3bd110482e8be5f68\interact.pep.xml" MINPROB=0.05" (SpectraST) init with SpectraST trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.5 RAPTURE rev 1, Build 201111141620 (MinGW)) AKeller@ISB read in 0 1+, 253 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20..... model complete after 26 iterations command completed in 0 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i C:\inetpub\wwwroot\tmp \1ecece635e644dd3bd110482e8be5f68\interact.pep.xml" Analyzing C:\inetpub\wwwroot\tmp \1ecece635e644dd3bd110482e8be5f68\interact.pep.xml ... Parsing search results "c:\inetpub\wwwroot\isb\data\APP\taskController \Ecolitest40177ed3cd9640da88fd867df9f85129\MsConvertplugin \97c355cdef384feba0e8c44fa943b921\output\fe_ecoli_mix1_081016_01 (SpectraST)"... => Total of 27 hits. => Total of 0 decoy hits. => Total of 0 excluded hits. Parsing search results "c:\inetpub\wwwroot\isb\data\APP\taskController \Ecolitest40177ed3cd9640da88fd867df9f85129\MsConvertplugin \97c355cdef384feba0e8c44fa943b921\output\fe_ecoli_mix2_081016_01 (SpectraST)"... => Total of 51 hits. => Total of 0 decoy hits. => Total of 0 excluded hits. util.c: Invalid argument util.c: Invalid argument util.c: Invalid argument command completed in 0 sec running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/inetpub/ wwwroot/tmp/1ecece635e644dd3bd110482e8be5f68/interact.pep.xml" c:/inetpub/wwwroot/tmp/1ecece635e644dd3bd110482e8be5f68/ interact.pep.xml(697) : error 17: XML Parsing error.XML or text declaration not at start of entityat l:697, c:0 This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/inetpub/ wwwroot/tmp/1ecece635e644dd3bd110482e8be5f68/interact.pep.xml" failed: No such process command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/inetpub/ wwwroot/tmp/1ecece635e644dd3bd110482e8be5f68/interact.pep.xml" exited with non-zero exit code: 3 -- 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.
