Hi,
after updating to GATK 3.8 I found the following ERROR in my log file.
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:f
ile:/dsk/data1/ngs/bin/GATK/3.8.0/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using Si
mpleLogger to log to the console...
I guess this is a bug. Might it be, that you forgot to add the library to the build?
Best,
Anselm Hoppmann