I'm getting a very similar error. Has anyone been able to resolve this yet?
> java -jar C:\TPP\bin\qualscore.jar -c 1.0 -p 0.1 .\interact.iproph.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 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000
13000 14000 15000 16000 17000 18000 1
9000 20000 21000 22000 23000 24000 25000 26000 27000 28000 29000
30000 31000 32000 33000 34000 35000 36
000 37000 38000 39000 40000 41000 42000 43000 44000 45000 46000
47000 48000 49000 50000 51000 52000 530
00 54000 55000 56000 57000 58000 59000 60000 61000 62000 63000
64000 65000 66000 67000 68000 69000 7000
0 71000 72000 73000 74000 75000 76000 77000 78000 79000 80000
81000 82000 83000 84000 85000 86000 87000
88000 88196
Interact data file contains 88195 entries.
0 +1 were removed.
Enumerating scans:
processing QEHF2175.mzXML...error: Parse error occurred - 9
java.lang.ArrayIndexOutOfBoundsException: 9
at org.isb.mzxml.MzXMLParser.convertMassList(MzXMLParser.java:384)
at org.isb.mzxml.MzXMLParser.endElement(MzXMLParser.java:312)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.
endElement(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.
XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.
XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.
next(Unknown Source)
at com.sun.org.apache.xerces.internal.impl.
XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.
parse(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.
parse(Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(
Unknown Source)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.
parse(Unknown Source)
at com.sun.org.apache.xerces.internal.jaxp.
SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.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
)
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
