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ERROR StatusLogger Log4j2 could not find a logging implementation
When I used GATK (version 3.8-0-ge9d806836) to generate GVCF with "HaplotypeCaller" tool, I got this error message:
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/Data/Sunhh/src/pipeline/gatk/GenomeAnalysisTK-3.8-0-g
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
I tested this with a very small bam file and got this message again, and the GATK program never ended.
Here is the detail information about the environment:
Operating system : Fedora 26 (4.12.5-300.fc26.x86_64);
GATK Version : 3.8-0-ge9d806836
JAVA version : Java(TM) SE Runtime Environment (build 1.8.0_144-b01) ; Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)
Variant calling from paired-end DNA-Seq Illumina reads ;
Command I used : /usr/java/jre1.8.0_144/bin/java -Xmx8G -jar /home/Sunhh/tools/GenomeAnalysisTK.jar -T HaplotypeCaller -R /Data/Sunhh/wm_reseqByPB/db/wm97pv0.scf.fa -I t_merged_dedup_pipe2.bam --genotyping_mode DISCOVERY -stand_call_conf 30 -ERC GVCF -o t_merged.g.vcf 1>s6.std.t_merged 2>s6.err.t_merged
If possible, I'd like to try some older version of GATK, but I don't know where to download them. Could you tell me how to get those old versions?