Hi GATK team!
we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this:
gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o /testsample.intervals
INFO 13:00:59,111 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 13:00:59,141 HelpFormatter - The Genome Analysis Toolkit (GATK) vnightly-2017-07-11-g1f763d5, Compiled 2017/07/11 00:01:14
INFO 13:00:59,141 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 13:00:59,142 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 13:00:59,142 HelpFormatter - [Thu Jul 20 13:00:58 UTC 2017] Executing on Linux 3.10.0-327.3.1.el7.x86_64 amd64
INFO 13:00:59,142 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11
INFO 13:00:59,170 HelpFormatter - Program Args: -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o /testsample.intervals
INFO 13:00:59,226 HelpFormatter - Executing as user on Linux 3.10.0-327.3.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11.
INFO 13:00:59,227 HelpFormatter - Date/Time: 2017/07/20 13:00:59
INFO 13:00:59,227 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 13:00:59,228 HelpFormatter - ---------------------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/opt/gatk/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console…
After this, the application unfortunately hangs. Running this with GATK v3.7 stable is also not working, we had issues with the bug in HaplotypeCallers VectorHMM library. Any ideas what we can do?