NoClassDefFoundError error during build of 2.4+ from gatk-protected repository

mlindermmlinderm Posts: 26Member


I am trying to build GATK w/ queue from HEAD of the gatk-protected repository (2a7af4316478348f7ea58e0803b3391593d6dbd6). I am getting the following error during the Queue extensions building phase:

[java] Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sting/commandline/MissingArgumentException [java] at org.broadinstitute.sting.commandline.CommandLineProgram.start( [java] at org.broadinstitute.sting.commandline.CommandLineProgram.start( [java] at org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator.main( [java] Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sting.commandline.MissingArgumentException [java] at$ [java] at Method) [java] at [java] at java.lang.ClassLoader.loadClass( [java] at sun.misc.Launcher$AppClassLoader.loadClass( [java] at java.lang.ClassLoader.loadClass( [java] ... 3 more

BUILD FAILED /hpc/users/lindem03/packages/gatk-mssm/dev/build.xml:509: Java returned: 1 at at at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke( at java.lang.reflect.Method.invoke( at at at at at at at at at at at at

When I run ant in debug mode I see the directory with the newly build GATK classes on classpath. Is there something else I might be missing. I am trying to upgrade from 1.6...




Best Answer


Sign In or Register to comment.