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java.lang.IncompatibleClassChangeError GATK 4
I hit an error with GATK 4 beta 6 using the RealignerTargetCreator - as a complete java newbie it's quite incomprehensible to me. I'm running (oracle) java 9.0.1(and thus GATK 3 RealignerTargetCreator isn't working for me either ).
Here is the command I ran:
gatk-launch RealignerTargetCreator -R ~/data/ref/hg38.fa -I Sample1_dedup.bam -o Sample1_int.intervals
And this is the output:
Using GATK jar /usr/local/bin/gatk-4.beta.6/gatk-package-4.beta.6-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /usr/local/bin/gatk-4.beta.6/gatk-package-4.beta.6-local.jar RealignerTargetCreator -R /home/jamie/data/ref/hg38.fa -I Sample1_dedup.bam -o Sample1_int.intervals Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/barclay/argparser/CommandLineProgramGroup. Method lambda$static$0(Lorg/broadinstitute/barclay/argparser/CommandLineProgramGroup;Lorg/broadinstitute/barclay/argparser/CommandLineProgramGroup;)I at index 43 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef at org.broadinstitute.barclay.argparser.CommandLineProgramGroup.<clinit>(CommandLineProgramGroup.java:16) at org.broadinstitute.hellbender.Main.printUsage(Main.java:332) at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:305) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:156) at org.broadinstitute.hellbender.Main.main(Main.java:239)