Hi, Does somebody has extensive experience with the qualscore tool and possibly knows a solution to the problem mentioned below? Many thanks in advance, Gerben
On Sep 28, 2010, at 12:41 , Gerben Menschaert wrote: > Hi all, > > By including the extra classes, the qualscore is working now. > > Still I encounter another problem. > > My workflow: > > MS/MS identification with Mascot server results in a *.dat file. > Conversion of the *.dat file to a *.pep.xml file (using the TPP pipeline). > Analyse peptides using xInteract to resulting interact.pep.xml file. > > Feeding this interact.pep.xml file to the quality scoring module gives the > following error, see below. > > > Does the qualscore only works within an identification pipeline performed > with Sequest as database search engine? > Normally only the interact.pep.xml file is needed as input to the qualscore, > apparently an mzXML file is also necessary and cannot be found (see below)? > > Many thanks in advance, > Gerben > > > Attempting to run the following program: > run_in c:/Inetpub/wwwroot/ISB/data; java -jar > c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 interact.isletspep.xml > > > QualScore version 1.0_2 Copyright (C) 2006 > Institute for Systems Biology, Seattle WA > QualScore is free software and comes with absolutely no warranty. > > XML > Loading interact data: > 61 > Interact data file contains 60 entries. > 0 +1 were removed. > Enumerating scans: > processing Tue_Sep_28_11-55-25_2010.mzXML...Problem finding offset index. > java.io.FileNotFoundException: > C:\Inetpub\wwwroot\ISB\data\Tue_Sep_28_11-55-25_2010.mzXML (The system cannot > find the file specified) > at java.io.FileInputStream.open(Native Method) > at java.io.FileInputStream.<init>(Unknown Source) > at org.isb.mzxml.MzXMLParser.getScanOffsetIndex(MzXMLParser.java:164) > at org.isb.mzxml.MzXML.<init>(MzXML.java:50) > at > org.systemsbiology.qualscore.SingleInteractXML.enumerateDtasFromMZXML(SingleInteractXML.java:85) > at > org.systemsbiology.qualscore.SingleInteractXML.enumerateScans(SingleInteractXML.java:71) > at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:197) > at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041) > error: Parse error occurred - > C:\Inetpub\wwwroot\ISB\data\Tue_Sep_28_11-55-25_2010.mzXML (The system cannot > find the file specified) > java.io.FileNotFoundException: > C:\Inetpub\wwwroot\ISB\data\Tue_Sep_28_11-55-25_2010.mzXML (The system cannot > find the file specified) > at java.io.FileInputStream.open(Native Method) > at java.io.FileInputStream.<init>(Unknown Source) > at java.io.FileInputStream.<init>(Unknown Source) > at sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source) > at sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown > Source) > at > com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(Unknown > Source) > at > com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown > Source) > at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown > Source) > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown > Source) > at javax.xml.parsers.SAXParser.parse(Unknown Source) > at javax.xml.parsers.SAXParser.parse(Unknown Source) > at org.isb.mzxml.MzXMLParser.getScans(MzXMLParser.java:128) > at org.isb.mzxml.MzXML.rapScans(MzXML.java:132) > at > org.systemsbiology.qualscore.SingleInteractXML.enumerateDtasFromMZXML(SingleInteractXML.java:91) > at > org.systemsbiology.qualscore.SingleInteractXML.enumerateScans(SingleInteractXML.java:71) > at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:197) > at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041) > Exception in thread "main" java.lang.NullPointerException > at > org.systemsbiology.qualscore.SingleInteractXML.enumerateDtasFromMZXML(SingleInteractXML.java:93) > at > org.systemsbiology.qualscore.SingleInteractXML.enumerateScans(SingleInteractXML.java:71) > at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:197) > at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041) > > command "java -jar c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 > interact.isletspep.xml" failed: Operation not permitted > > > > On Sep 24, 2010, at 22:04 , David Shteynberg wrote: > >> Everything you need to run qualscore should be here: >> >> http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/lib/ >> >> -David >> >> On Fri, Sep 24, 2010 at 12:08 PM, Vishal Swaroop <[email protected]> >> wrote: >>> It is also important to know which version of JFreechart is used by >>> qualscore. >>> Quick view of qualscore main class shows import of >>> "org.jfree.data.SeriesDataset' which I was able to find in >>> "jfreechart-0.9.19" but other import (org.jfree.chart.Marker) was not >>> available. >>> >>> When I tried latest version "jfreechart-1.0.13", main class of qualscore >>> was not able to find number of the imports ( >>> org.jfree.chart.Marker, org.jfree.data.CombinedDataset, >>> org.jfree.data.SeriesDataset... etc.) >>> Thanks >>> Vishal >>> >>> >>> >>> >>> On Fri, Sep 24, 2010 at 2:33 PM, Vishal Swaroop <[email protected]> >>> wrote: >>>> >>>> Hi Gerben, >>>> I realized that you are missing jfreechart jar in classpath, is it not >>>> included with TPP_Setup_v4_4.... , check if it is available under >>>> c:\Inetpb\tpp-bin.... if not then then you can try downloading it and set >>>> it >>>> in classpath. >>>> Thanks >>>> >>>> >>>> On Fri, Sep 24, 2010 at 9:20 AM, Gerben Menschaert >>>> <[email protected]> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> Is anybody using the QualScore module within the TPP? Is it still in >>>>> use? >>>>> >>>>> Running it gave me the following error: >>>>> >>>>> run_in c:/Inetpub/wwwroot/ISB/data; java -jar c:\Inetpub\tpp-bin >>>>> \qualscore.jar -c 1.0 -p 0.1 F026703.pep.xml >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> java.lang.NoClassDefFoundError: org/jfree/data/SeriesDataset >>>>> Caused by: java.lang.ClassNotFoundException: >>>>> org.jfree.data.SeriesDataset >>>>> at java.net.URLClassLoader$1.run(Unknown Source) >>>>> at java.security.AccessController.doPrivileged(Native Method) >>>>> at java.net.URLClassLoader.findClass(Unknown Source) >>>>> at java.lang.ClassLoader.loadClass(Unknown Source) >>>>> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) >>>>> at java.lang.ClassLoader.loadClass(Unknown Source) >>>>> Could not find the main class: >>>>> org.systemsbiology.qualscore.commandline.Main. Program will exit. >>>>> Exception in thread "main" >>>>> command "java -jar c:\Inetpub\tpp-bin\qualscore.jar -c 1.0 -p 0.1 >>>>> F026703.pep.xml" failed: Operation not permitted >>>>> Command FAILED >>>>> >>>>> >>>>> I'm using the latest version of the TPP version >>>>> (TPP_Setup_v4_4_VUVUZELA_rev_1_RC2.exe). >>>>> >>>>> >>>>> Many thanks in advance, >>>>> Kind regards, >>>>> Gr.ben >>>>> >>>>> -- >>>>> 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. >>>>> >>>> >>> >>> -- >>> 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. >>> >> >> -- >> 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. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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