GATK 3.8 logger ERROR

HoppmannHoppmann FreiburgMember

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

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @hemp @Hoppmann
    Hi,

    They are looking to fix this in GATK3 as well. You can find updates in this thread.

    -Sheila

  • I also have same issue as below.

    java -jar ./GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fa -I B16031713275-CLN.sorted.rmdup.realigned.recal.bam -o B16031713275-CLN.sorted.rmdup.realigned.recal.bam.vcf
    INFO 15:07:14,039 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 15:07:14,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
    INFO 15:07:14,043 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
    INFO 15:07:14,043 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
    INFO 15:07:14,044 HelpFormatter - [Thu Sep 07 15:07:14 CST 2017] Executing on Linux 2.6.32-696.3.2.el6.x86_64 amd64
    INFO 15:07:14,044 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01
    INFO 15:07:14,051 HelpFormatter - Program Args: -T HaplotypeCaller -R hg19.fa -I B16031713275-CLN.sorted.rmdup.realigned.recal.bam -o B16031713275-CLN.sorted.rmdup.realigned.recal.bam.vcf
    INFO 15:07:14,056 HelpFormatter - Executing as [email protected] on Linux 2.6.32-696.3.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01.
    INFO 15:07:14,057 HelpFormatter - Date/Time: 2017/09/07 15:07:14
    INFO 15:07:14,057 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 15:07:14,057 HelpFormatter - ----------------------------------------------------------------------------------
    ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/home/wfz/workspace/Geno_Mutations/TangZhiHong/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 15:07:14,242 GenomeAnalysisEngine - Deflater: IntelDeflater
    INFO 15:07:14,242 GenomeAnalysisEngine - Inflater: IntelInflater
    INFO 15:07:14,243 GenomeAnalysisEngine - Strictness is SILENT

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Feizhen_Wu
    Hi,

    This should be fixed in the latest nightly build :smiley:

    -Sheila

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