Hi,
While running the tool "Realigner Target Creator" on cloudman I encounter the following error. I TRIED running using on a node with high memory. It gave me the same error. Can anyone help me to rectify this?
Thank You!
java.lang.ExceptionInInitializerError at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.<init>(GenomeAnalysisEngine.java:143) at org.broadinstitute.sting.gatk.CommandLineExecutable.<init>(CommandLineExecutable.java:50) at org.broadinstitute.sting.gatk.CommandLineGATK.<init>(CommandLineGATK.java:53) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:89) Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from Accessible.class at org.reflections.Reflections.scan(Reflections.java:166) at org.reflections.Reflections.<init>(Reflections.java:91) at org.broadinstitute.sting.utils.classloader.PluginManager.<clinit>(PluginManager.java:79) ... 4 more Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: could not create class file from Accessible.class at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.reflections.Reflections.scan(Reflections.java:162) ... 6 more Caused by: java.lang.RuntimeException: could not create class file from Accessible.class at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:41) at org.reflections.Reflections$2.run(Reflections.java:149) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.IOException: invalid constant type: 18 at javassist.bytecode.ConstPool.readOne(ConstPool.java:1023) at javassist.bytecode.ConstPool.read(ConstPool.java:966) at javassist.bytecode.ConstPool.<init>(ConstPool.java:127) at javassist.bytecode.ClassFile.read(ClassFile.java:693) at javassist.bytecode.ClassFile.<init>(ClassFile.java:85) at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:86) at org.reflections.adapters.JavassistAdapter.createClassObject(JavassistAdapter.java:22) at org.reflections.scanners.AbstractScanner.scan(AbstractScanner.java:38) ... 6 more
