If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Gatk haplotype caller java error

Hello GATK team,

I am trying to run gatk haplotypecaller (version on a bam file and used the following command:

"java -jar /ufrc/gatk-
-T HaplotypeCaller
-R /ufrc/EquCab3.0_UCSC/equCab3.fa
-I AMH.sorted.dedup.bam
-O AMH.g.vcf.gz

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$0(Lorg/broadinstitute/barclay/argparser/ CommandLineProgramGroup;Lorg/broadinstitute/barclay/argparser/
CommandLineProgramGroup;)I at index 43 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
at org.broadinstitute.barclay.argparser.Comm
andLineProgramGroup.( at org.broadinstitute.hellbender.Main.printUsage(
at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main$ at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(M$ at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(
/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



Sign In or Register to comment.