Java 17 Exception #3
Description
Hello,
Thank you for developing a tool for quant and visualization of isobaric data. I am trying to test out the application on a Windows 11 machine using your test files and having trouble with a Java error. The only version of java I have installed is Java 17 JDK and verified with "java --version".
java 17.0.3.1 2022-04-22 LTS
Java(TM) SE Runtime Environment (build 17.0.3.1+2-LTS-6)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.3.1+2-LTS-6, mixed mode, sharing)
I have re-installed java jdk from the link in your online documentation, but am still getting the error below when running it from the command line. I have tried the GUI, however it doesn't appear to be processing the file (I have waited for 20 min), so I imagine it's running into this error as well?
I also wanted to ask about whether isobaricquant supports multiple mzml files, such as from pre-fractionated datasets. I noticed the hits file has a parameter "Search ID" which seems to indicate that PSMs from different search files may be supported?
Thanks for your assistance.
Todd
java -jar C:\Data\IQ\IsobaricQuant_WIN.jar -c C:\Data\IQ\config_OT_MS2-TMTpro.conf -mzf C:\Data\IQ\a18182_MS2_1.mzML -h C:\Data\IQ\a18182_MS2_1_hits.csv -o C:\Data\IQ
Reading configuration file...
Quantifying...
Writing output in C:\Data\IQ
MzMLFile filePath: C:\Data\IQ\a18182_MS2_1.mzML
Exception in thread "main" java.lang.ExceptionInInitializerError
at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:77)
at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:114)
at com.sun.xml.bind.v2.runtime.reflect.Accessor$GetterSetterReflection.optimize(Accessor.java:366)
at com.sun.xml.bind.v2.runtime.property.ArrayProperty.(ArrayProperty.java:65)
at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.(ArrayERProperty.java:84)
at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.(ArrayElementProperty.java:96)
at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.(ArrayElementNodeProperty.java:58)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:124)
at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.(ClassBeanInfoImpl.java:171)
at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:481)
at com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:315)
at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:139)
at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:117)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:211)
at javax.xml.bind.ContextFinder.find(ContextFinder.java:372)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:574)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:522)
at javax.xml.bind.JAXB$Cache.(JAXB.java:87)
at javax.xml.bind.JAXB.getContext(JAXB.java:114)
at javax.xml.bind.JAXB.unmarshal(JAXB.java:143)
at uk.ac.ebi.jmzml.MzMLElement.loadProperties(MzMLElement.java:609)
at uk.ac.ebi.jmzml.MzMLElement.(MzMLElement.java:564)
at uk.ac.ebi.jmzml.MzMLElement.(MzMLElement.java:83)
at uk.ac.ebi.jmzml.xml.Constants.(Constants.java:56)
at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory$MzMlIndexerImpl.(MzMLIndexerFactory.java:82)
at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory$MzMlIndexerImpl.(MzMLIndexerFactory.java:52)
at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory.buildIndex(MzMLIndexerFactory.java:49)
at uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller.(MzMLUnmarshaller.java:121)
at uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller.(MzMLUnmarshaller.java:100)
at villeninputs.input.spectroscopy.MzMLFile.(MzMLFile.java:67)
at villeninputs.input.spectroscopy.MzFileFactory.create(MzFileFactory.java:34)
at edu.uw.villenlab.isobaricquant.Quantification.quantify(Quantification.java:1027)
at edu.uw.villenlab.isobaricquant.IsobaricQuant.main(IsobaricQuant.java:98)
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @56a6d5a6
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199)
at java.base/java.lang.reflect.Method.setAccessible(Method.java:193)
at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:150)
at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:147)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.(Injector.java:146)
... 42 more