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.
