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.
