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Gatk haplotype caller java error
Hello GATK team,
I am trying to run gatk haplotypecaller (version 220.127.116.11) on a bam file and used the following command:
"java -jar /ufrc/gatk-18.104.22.168/gatk-package-22.214.171.124-local.jar
However, I keep getting the java related error below that I cannot understand. Is there something wrong with my command?
The error is:
Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/barclay/argparser/CommandLineProgramGroup8. Method lambda$static$0(Lorg/broadinstitute/barclay/argparser/ CommandLineProgramGroup;Lorg/broadinstitute/barclay/argparser/
CommandLineProgramGroup;)I at index 43 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
andLineProgramGroup.(CommandLineProgramGroup.java:19) at org.broadinstitute.hellbender.Main.printUsage(Main.java:384)
at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main$ at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(M$ at org.broadinstitute.hellbender.Main.mainEntry(Main.java:204)
/tmp/slurmd/job40546019/slurm_script: line 26: -T: command not found /tmp/slurmd/job40546019/slurm_script: line 27: -R: command not found
/tmp/slurmd/job40546019/slurm_script: line 28: -I: command not found
/tmp/slurmd/job40546019/slurm_script: line 29: -O: command not found
/tmp/slurmd/job40546019/slurm_script: line 30: -ERC: command not found