Hi there,
Is it possible that mac and or java 9 are not happy with the gatk wrapper?
Thanks in advance
Stephane
$ gatk --list
Using GATK jar /opt/biotools/gatk-4.0.0.0/gatk-package-4.0.0.0-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=1 -jar /opt/biotools/gatk-4.0.0.0/gatk-package-4.0.0.0-local.jar --help
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:19)
at org.broadinstitute.hellbender.Main.printUsage(Main.java:366)
at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:326)
at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:172)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:192)
at org.broadinstitute.hellbender.Main.main(Main.java:275)
$ java --version
java 9.0.1
Java(TM) SE Runtime Environment (build 9.0.1+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.1+11, mixed mode)
$ picard: Version: 2.17.4-SNAPSHOT