Hi Damon, I wonder if this has something to do with this index mismatch:
XML Loading interact data: 1000 2000 3000 4000 5000 6000 7000 8000 9000 9721 Interact data file contains 9720 entries. I am not sure why but notice that the entries are off by one. Perhaps that is a clue to the error, which in fact claims an array overrun? Can you count the entries in your files? -David On Thu, Apr 21, 2016 at 11:14 AM, Damon May <[email protected]> wrote: > I'd like to use qualscore from the command line on some pepXML and mzXML > files, but I'm running into an mzXML-parsing problem. Full output of > qualscore when run on my interact.pep.xml file is pasted below. > > The mzML file in question was converted from a QE raw file using msConvert > 3.0.9576 with default arguments. I can search it with Comet, and msInspect > (which also uses JRAP) parses it just fine. > > I'm using qualscore version 1.0_3, downloaded from here: > > https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/qualscore/ > > Specifically, I grabbed qualscore.v1.0_3.jar, jcommon-0.9.0.jar and > jfreechart-0.9.20.jar. Did I get that right? (BTW, as you can see in the > output below, qualscore.v1.0_3.jar prints out a message saying it's version > 1.0_2) > > I've tried the same thing with qualscore.v1.0_2.jar, jcommon-0.9.0.jar, > jfreechart-0.9.15.jar and tar.jar, with output that looks identical except > for individual line numbers. > > Is there any fix or workaround you can think of? I tried to convert to > mzML and use that instead, but it appears to only look for mzXML files with > a name match. Is there any other file format I can try, to work around the > parsing issue? > > I'm happy to provide the data files in question, but of course they're > quite large. If no workaround springs to mind and you're willing to try to > reproduce it, I can put the files somewhere where you can grab them. > > Thanks! qualscore output is below. > > > 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 9721 > Interact data file contains 9720 entries. > 0 +1 were removed. > Enumerating scans: > processing 2014_Aug_18_QE18.mzXML...error: Parse error occurred - 93 > java.lang.ArrayIndexOutOfBoundsException: 93 > 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(AbstractSAXParser.java:609) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2973) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) > at > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649) > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:333) > at javax.xml.parsers.SAXParser.parse(SAXParser.java:328) > 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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