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.
