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
>>>>
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>>>>
>>>
>>
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