Unable to generate VCF

Question

[arshiya.g02]

am unable to generate vcf file and countering this error even after using AddReadGroups. can anyone help me to get through this ? Am getting this error

sudo ./gatk Mutect2 -R /home/arshiya/efs/FastQC/hg38.fa -I /home/arshiya/efs/FastQC/Read.bam -O /home/arshiya/efs/FastQC/Read.vcf.gz
Using GATK jar /home/arshiya/gatk-4.1.2.0/gatk-package-4.1.2.0-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=2 -jar /home/arshiya/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar Mutect2 -R /home/arshiya/efs/FastQC/hg38.fa -I /home/arshiya/efs/FastQC/Read.bam -O /home/arshiya/efs/FastQC/Read.vcf.gz

[July 22, 2019 at 8:30:25 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=343932928
Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/hellbender/transformers/ReadTransformer. Method lambda$identity$d67512bf$1(Lorg/broadinstitute/hellbender/utils/read/GATKRead;)Lorg/broadinstitute/hellbender/utils/read/GATKRead; at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
    at org.broadinstitute.hellbender.transformers.ReadTransformer.identity(ReadTransformer.java:30)
    at org.broadinstitute.hellbender.engine.GATKTool.makePreReadFilterTransformer(GATKTool.java:345)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:276)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)

[finswimmer]

Never, NEVER use sudo to run a program, unless you know what you are doing. With sudo you give your program administrator privileges and this is only necessary for system relevant applications.

Answer 1

[Pierre Lindenbaum]

what is your java version ?

java -version

it should be something like '1.8' if it's 11 or over then you're using the wrong version of java. https://software.broadinstitute.org/gatk/documentation/quickstart.php

[arshiya.g02]

openjdk version "11.0.3" 2019-04-16
OpenJDK Runtime Environment (build 11.0.3+7-Ubuntu-1ubuntu218.04.1)
OpenJDK 64-Bit Server VM (build 11.0.3+7-Ubuntu-1ubuntu218.04.1, mixed mode, sharing)

[Pierre Lindenbaum]

https://software.broadinstitute.org/gatk/documentation/quickstart.php

Make sure you have Java 8 / JDK 1.8 (Oracle or OpenJDK, doesn't matter).

install java 1.8, change your ${PATH} and your ${ JAVA_HOME} variables and retry