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Java error when using ASEReadCounter
I'm trying to do an allele-specific expression analysis on some of my samples and I gave ASEReadCounter a try. I'm having trouble with Java and I probably should post this on some java forum but thought you could help me since you would know better about GATK. Here is the error message I get:
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/spark/Partitioner at java.lang.Class.getDeclaredConstructors0(Native Method) at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671) at java.lang.Class.getConstructors(Class.java:1651) at org.broadinstitute.hellbender.utils.ClassUtils.canMakeInstances(ClassUtils.java:30) at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:318) at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:180) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:202) at org.broadinstitute.hellbender.Main.main(Main.java:289) Caused by: java.lang.ClassNotFoundException: org.apache.spark.Partitioner at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 8 more
At first I tried it using Java version 9. I thought this could be the problem, so I tried running it using Java 8 but that didn't solve it. Could you help me?