mzML Parser Class Fails to Initialize

[mobiusklein]

Attempting to run MS-GF+ under Java 9.0.1 on an mzML file produced by ProteoWizard MSConvert 30.11626 produces the following traceback:

Reading spectra...
Exception in thread "main" java.lang.ExceptionInInitializerError
        at uk.ac.ebi.jmzml.xml.Constants.<clinit>(Constants.java:56)
        at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory$MzMlIndexerImpl.<init>(MzMLIndexerFactory.java:82)
        at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory$MzMlIndexerImpl.<init>(MzMLIndexerFactory.java:52)
        at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory.buildIndex(MzMLIndexerFactory.java:49)
        at uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller.<init>(MzMLUnmarshaller.java:121)
        at uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller.<init>(MzMLUnmarshaller.java:100)
        at edu.ucsd.msjava.mzml.MzMLAdapter.<init>(MzMLAdapter.java:27)
        at edu.ucsd.msjava.msutil.SpectraAccessor.getSpecMap(SpectraAccessor.java:38)
        at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:217)
        at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:105)
        at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:56)
Caused by: javax.xml.bind.DataBindingException: javax.xml.bind.JAXBException
 - with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
        at javax.xml.bind.JAXB.unmarshal(JAXB.java:186)
        at uk.ac.ebi.jmzml.MzMLElement.loadProperties(MzMLElement.java:609)
        at uk.ac.ebi.jmzml.MzMLElement.<init>(MzMLElement.java:564)
        at uk.ac.ebi.jmzml.MzMLElement.<clinit>(MzMLElement.java:83)
        ... 11 more
Caused by: javax.xml.bind.JAXBException
 - with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
        at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:241)
        at javax.xml.bind.ContextFinder.find(ContextFinder.java:455)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:652)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:599)
        at javax.xml.bind.JAXB$Cache.<init>(JAXB.java:127)
        at javax.xml.bind.JAXB.getContext(JAXB.java:154)
        at javax.xml.bind.JAXB.unmarshal(JAXB.java:183)
        ... 14 more
Caused by: java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(Unknown Source)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(Unknown Source)
        at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
        at javax.xml.bind.ContextFinder.safeLoadClass(ContextFinder.java:573)
        at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:239)
        ... 20 more

While search can be performed if I use mzXML instead, when attempting to write the mzIdentML file a similar error:

Writing results...
Exception in thread "main" java.lang.ExceptionInInitializerError
        at uk.ac.ebi.jmzidml.model.utils.ModelConstants.<clinit>(ModelConstants.java:50)
        at uk.ac.ebi.jmzidml.xml.jaxb.marshaller.MarshallerFactory.initializeMarshaller(MarshallerFactory.java:37)
        at uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller.marshal(MzIdentMLMarshaller.java:100)
        at uk.ac.ebi.jmzidml.xml.io.MzIdentMLMarshaller.marshal(MzIdentMLMarshaller.java:91)
        at edu.ucsd.msjava.mzid.MZIdentMLGen.writeResults(MZIdentMLGen.java:143)
        at edu.ucsd.msjava.mzid.MZIdentMLGen.writeResultsOriginal(MZIdentMLGen.java:130)
        at edu.ucsd.msjava.mzid.MZIdentMLGen.writeResultsCleanerTempFile(MZIdentMLGen.java:214)
        at edu.ucsd.msjava.mzid.MZIdentMLGen.writeResults(MZIdentMLGen.java:113)
        at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:387)
        at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:105)
        at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:56)
Caused by: javax.xml.bind.DataBindingException: javax.xml.bind.JAXBException
 - with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
        at javax.xml.bind.JAXB.unmarshal(JAXB.java:186)
        at uk.ac.ebi.jmzidml.MzIdentMLElement.loadProperties(MzIdentMLElement.java:1103)
        at uk.ac.ebi.jmzidml.MzIdentMLElement.<init>(MzIdentMLElement.java:990)
        at uk.ac.ebi.jmzidml.MzIdentMLElement.<clinit>(MzIdentMLElement.java:40)
        ... 11 more
Caused by: javax.xml.bind.JAXBException
 - with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory]
        at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:241)
        at javax.xml.bind.ContextFinder.find(ContextFinder.java:455)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:652)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:599)
        at javax.xml.bind.JAXB$Cache.<init>(JAXB.java:127)
        at javax.xml.bind.JAXB.getContext(JAXB.java:154)
        at javax.xml.bind.JAXB.unmarshal(JAXB.java:183)
        ... 14 more
Caused by: java.lang.ClassNotFoundException: com.sun.xml.internal.bind.v2.ContextFactory
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(Unknown Source)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(Unknown Source)
        at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
        at javax.xml.bind.ContextFinder.safeLoadClass(ContextFinder.java:573)
        at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:239)
        ... 20 more

This appears to be resolved by adding --add-modules java.xml.bind to the java command line argument list before the jar file. Am I using an unsupported version of Java or can this be added to the build step to remove the need to specify it at run time?

[FarmGeek4Life]

This might be an issue with the version of java - I have yet to try running it with Java 9, it is compiled against the Java 6 baseline, and I have always run it under Java 7 and Java 8. Yes, it appears that Java 9 removed some classes that are used by the mzML/mzIdentML reader/writer dependencies used by MS-GF+. Please try running with Java 8 for confirmation.

[mobiusklein]

Yes, this is an issue of using too new a version of Java. Java 8 seems to work fine.

[FarmGeek4Life]

I was able to resolve this issue by adding two new dependencies to MS-GF+, as of release v2018.01.30. They are marked as deprecated in Java 9, with plans to remove them in the future in favor of making them separate packages. The --add-modules=java.xml.bind,java.activation JVM option should work for prior releases, but it's more confusing to users.

[glormph]

Hmm I'm on openJDK 11 with the 2017.07.21 and I get

java -jar --add-modules=java.xml.bind,java.activation  msgf_plus-2017.07.21-1/MSGFPlus.jar
Error occurred during initialization of boot layer
java.lang.module.FindException: Module java.xml.bind not found

Maybe the openJDK is too new?

[FarmGeek4Life]

A change request removing java.xml.bind from the classes built-in to OpenJDK/Java 11 was accepted (it was deprecated as of OpenJDK/Java 9). This will likely mean that only MS-GF+ v2018.01.30 and newer will work with Java 11. The previous --add-modules=java.xml.bind,java.activation workaround will no longer work because the package does not exist in OpenJDK/Java 11.