Hello Damian,
Just like Bjorn, I had the same error running the qualscore module, stating
that an mzXML cannot be found. Using the dta2XML on the generated *.dta files
and storing in the tpp-bin folder solves the problem.
Let me briefly describe the workflow:
1) Starting material = peptide fragmentation MS in mgf format.
2) Running Mascot results in a F026703.dat file
3) Running xinteract:
Command:
C:\Inetpub\tpp-bin>xinteract.exe
-DC:\Inetpub\wwwroot\ISB\data\Mouse_peptides_20091008.fasta
-NC:\Inetpub\wwwroot\ISB\data\F026703.interact.pep.xml -eN -p0
C:\Inetpub\wwwroot\ISB\data\F026703.dat
Results in:
F026703.interact.pep.xml.index
f026703.interact.pep.xml
F026703.interact.pep.xsl
F026703.interact.pep.shtml
F026703.pep.xml
F026703.tgz
4) Running qualscore:
Command:
C:\Inetpub\wwwroot\ISB\data>java -jar qualscore.jar
C:\Inetpub\wwwroot\ISB\data\f026703.interact.pep.xml
Output: see below
Apparently the qualscore also requires a Mon_Oct_25_11-10-30_2010.mzXML next
tot the pep.xml file. Running the xinteract, the mascot F026703.dat file is
first transformed to a F026703.pep.xml file. Together an F026703.tgz zipped
file is created holding all the peaklist files in DTA format of all the
identified peptides (e.g. Mon_Oct_25_11-10-30_2010.spectrum66.0000.0000.3.dta).
You can tar -xzvf this file and use the dta2XML tool (within the TPPipeline) to
convert to the correct Mon_Oct_25_11-10-30_2010.mzXML file.
If you store this mzXML in the tpp-bin folder, the qualscore seems to work.
Gr.ben
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:
180
Interact data file contains 179 entries.
43 +1 were removed.
Enumerating scans:
processing Mon_Oct_25_11-10-30_2010.mzXML...Problem finding offset index.
java.io.FileNotFoundException: C:\Inetpub\tpp-bin\Mon_Oct_25_11-10-30_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:88)
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\tpp-bin\Mon_Oct_25_11-10-30_2010.mzXML(The system cannot find the
file specified)
java.io.FileNotFoundException:
C:\Inetpub\tpp-bin\Mon_Oct_25_11-10-30_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)
On Oct 24, 2010, at 04:40 , GATTACA wrote:
> We still use Qualscore on linux. I've had problems running it on
> Apple's OS (I have no explanation why).
>
> my 'qualscore' folder contains:
> qualscore_v1.0_2.jar
> lib
>
> The 'lib' folder must be in the same folder as the JAR file in order
> for qualscore.jar to run.
> Alternatively you could write a quick bash script to reduce on
> typing.
>
> I have successfully used Qualscore with Sequest results and Mascot
> results. However we mostly use XTANDEM in our lab.
>
> When you run xinteract do you use the '-p0' option? (that' -
> p<the_number_zero>). This is essential for qualscore to work.
> Also, check the version of java you are using. I think you HAVE to use
> Oracle's version of JAVA. The some of the other flavors of JAVA won't
> work.
>
> I've gotten the error messages above before but I can't remember the
> reason. If using the -p0 option doesn't solve it, can you send me one
> of your results files and the mzXML file that goes with it?
>
> Hope this helps.
>
> Damian
>
>
> On Oct 23, 3:22 pm, "[email protected]" <[email protected]> wrote:
>> We still use this tool from time to time. I will ask Damian in my
>> group to take a look at this post to see if he can identify the
>> problem.
>>
>> Alexey Nesvizhskii
>> University of Michigan
>>
>> On Oct 8, 10:41 am, Bjorn <[email protected]> wrote:
>>
>>> I tried to get Qualscore to work on the Mac command line, but got
>>> this
>>
>>> bvictor$ java -jar /usr/local/tpp/bin/qualscore.v1.0_2.jar
>>> P01080_24h_gamma_decoy_cRAP.pep.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:
>>> 857
>>> Interact data file contains 856 entries.
>>> 12 +1 were removed.
>>> Enumerating scans:
>>> processing 100920.mzXML...Problem finding offset index.
>>> java.io.FileNotFoundException: /Library/WebServer/Documents/thegpm/tpp/
>>> data/P01080_Zambia5/CID/100920.mzXML (No such file or directory)
>>> at java.io.FileInputStream.open(Native Method)
>>> at java.io.FileInputStream.<init>(FileInputStream.java:106)
>>> 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 - /Library/WebServer/Documents/thegpm/tpp/
>>> data/P01080_Zambia5/CID/100920.mzXML (No such file or directory)
>>> java.io.FileNotFoundException: /Library/WebServer/Documents/thegpm/tpp/
>>> data/P01080_Zambia5/CID/100920.mzXML (No such file or directory)
>>> at java.io.FileInputStream.open(Native Method)
>>> at java.io.FileInputStream.<init>(FileInputStream.java:106)
>>> at java.io.FileInputStream.<init>(FileInputStream.java:66)
>>> at
>>> sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:
>>> 70)
>>> at
>>> sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection....
>>> 161)
>>> at
>>> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:
>>> 653)
>>> at
>>> com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:
>>> 186)
>>> at
>>> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
>>> 772)
>>> at
>>> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
>>> 737)
>>> at
>>> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
>>> 119)
>>> at
>>> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
>>> 1205)
>>> at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
>>> $JAXPSAXParser.parse(SAXParserImpl.java:522)
>>> at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
>>> at javax.xml.parsers.SAXParser.parse(SAXParser.java:331)
>>> 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)
>>
>>> somewhere in the beginning I see this:
>>> FileNotFoundException: /Library/WebServer/Documents/thegpm/tpp/data/
>>> P01080_Zambia5/CID/100920.mzXML (No such file or directory)
>>
>>> This file does indeed not exist. There are many files for the pep.xml
>>> file and they are all called something like this:
>>> 100920.LC6.IT6.XX.P01080_2-A.10_01_2701.mzXML
>>> 100920.LC6.IT6.XX.P01080_2-A.11_01_2702.mzXML
>>> etc...
>>
>>> Is that where Qualscore is tripping over?
>>
>>> To be honest, I still don't know where I am supposed to put the lib
>>> folder and qualscore.v1.0_2.jar file. I just tried something...
>>> Can anyone please tell me where they store the lib and
>>> qualscore.v1.0_2.jar file on a Mac system??
>>
>>> Many thanks!
>>
>>> bjorn
>
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