Apparently something is still going wrong while creating the mzXML file. The tool tries to scan through the Mon_Oct_25_15-56-04_2010.mzXML file but only seems to retrieve information for one fragmentation spectrum.
C:\Inetpub\tpp-bin>java -jar qualscore.jar c:\Inetpub\wwwroot\ISB\data\F027342\f027342.interact.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: 1000 1390 Interact data file contains 1389 entries. 589 +1 were removed. Enumerating scans: processing Mon_Oct_25_15-56-04_2010.mzXML... 1 Features calculated for: 1 (219 ms) Training set: 0/1 (good/bad) Unassigned spectra: 1 ERROR: Training set distribution unusable. Any ideas? Gr.ben On Oct 25, 2010, at 15:49 , Gerben Menschaert wrote: > 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 >> >> -- >> 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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