Hi I'm trying to run
java -jar install/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -T RealignerTargetCreator -R GCF_008822105.2_bTaeGut2.pat.W.v2_genomic.fa -I dedup_RSFV1A.bam -o RSFV1A_realtarget.list

But get this error and process is killed or core dumped in the end

INFO  15:36:31,585 HelpFormatter - ----------------------------------------------------------------------------------
INFO  15:36:31,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO  15:36:31,587 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO  15:36:31,588 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO  15:36:31,589 HelpFormatter - [Tue Jul 07 15:36:31 EDT 2020] Executing on Linux 3.10.0-957.5.1.el7.x86_64 amd64
INFO  15:36:31,589 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14
INFO  15:36:31,592 HelpFormatter - Program Args: -T RealignerTargetCreator -R /users/mfariasv/data/mfariasv/newzf20/GCF_008822105.2_bTaeGut2.pat.W.v2_genomic.fa -I /users/mfariasv/data/mfariasv/aligned_newZFV2/dedup/dedup_RSFV1A.bam -o /users/mfariasv/data/mfariasv/aligned_newZFV2/realign/RSFV1A_realtarget.list
INFO  15:36:31,595 HelpFormatter - Executing as mfariasv@node1310.oscar.ccv.brown.edu on Linux 3.10.0-957.5.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14.
INFO  15:36:31,595 HelpFormatter - Date/Time: 2020/07/07 15:36:31
INFO  15:36:31,596 HelpFormatter - ----------------------------------------------------------------------------------
INFO  15:36:31,596 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/gpfs/data/ehuertas/mfariasv/install/GenomeAnalysisTK-3.8-0-ge9d806836/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...
INFO  15:36:31,737 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO  15:36:31,737 GenomeAnalysisEngine - Inflater: IntelInflater
INFO  15:36:31,738 GenomeAnalysisEngine - Strictness is SILENT
INFO  15:36:32,014 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  15:36:32,020 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  15:36:32,079 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
INFO  15:36:32,239 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO  15:36:32,630 GenomeAnalysisEngine - Done preparing for traversal
INFO  15:36:32,631 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  15:36:32,631 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  15:36:32,632 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime