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.java:
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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