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ERROR StatusLogger Log4j2 could not find a logging implementation

Hi developers,

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?

Thanks!

Best
Honghe

Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sunhh
    Hi Honghe,

    Can you test the latest nightly build? I think this issue is fixed in it. If not, I know there should be another patch release coming out that may fix this issue.

    -Sheila

  • @Sheila,

    I got the same error messages, but the program finished fine and I did see "done" in the error file. Are the ERROR messages a problem?

    Error messages I got are -

    ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/home/yin168/bin/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...

    How can I download the latest nightly build?

    I tried gatk 4, but I was unable to figure out corresponding components for commands gatk 3.8.0.

    The gatk 3.8.0 command is:

    java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ref.fasta -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

    What the corresponding command for gatk 4?

    Thanks.

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @XiaoshenYin

    Here is the link to the latest version of SplitNCigarReads tool.

    Regards
    Bhanu

  • XiaoshenYinXiaoshenYin Member
    edited November 21

    Hi @bhanuGandham,

    The command provided in the gatk RNAseq variant calling pipeline for SplitNcigarReads is:

    java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ref.fasta -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

    so what are corresponding parameters/comonents for (1) -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 and (2) -U ALLOW_N_CIGAR_READS in the latest version of SplitNCigarReads tool and gatk 4. Sorry, I read relevant documentations multiple times, but was unable to find them. Or, with the new version of SplitNcigarReads and gatk4, I do not need to set those two parameters?

    I would greatly appreciate it if you could help me figure that out.

    Thanks.

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @XiaoshenYin

    That's correct, with the new version of SplitNcigarReads and gatk4, you do not need to set those two parameters.

    Regards
    Bhanu

  • XiaoshenYinXiaoshenYin Member

    Hi @bhanuGandham ,

    When I use the old version gatk 3, I got the error messages, but the program finished fine and I did see "done" in the error file.

    Error messages I got are -

    ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/home/yin168/bin/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...

    Do these two ERROR messages matter? Can I still use the old version gatk 3, instead of gatk 4, to do SplitNcigarReads if the program/script finished fine but these two ERROR messages were generated? Or, do I have to use gatk 4 to avoid these ERROR messages?

    Thanks.

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @XiaoshenYin

    We recommend you use gatk4 as it is new and improved and has the bug fixes from the previous versions.

    Regards
    Bhanu

  • XiaoshenYinXiaoshenYin Member

    Hi @bhanuGandham @shlee ,

    When doing the step "Split'N'Trim and reassign mapping qualities", gatk 4 cannot do the important tweak below:

    At this step we also add one important tweak: we need to reassign mapping qualities, because STAR assigns good alignments a MAPQ of 255 (which technically means “unknown” and is therefore meaningless to GATK). So we use the GATK’s ReassignOneMappingQuality read filter to reassign all good alignments to the default value of 60. This is not ideal, and we hope that in the future RNAseq mappers will emit meaningful quality scores, but in the meantime this is the best we can do. In practice we do this by adding the ReassignOneMappingQuality read filter to the splitter command. (This paragraph is extracted from gatk RNAseq variant calling pipeline)

    In gatk 4, I am unable to find corresponding parameters for "-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS" and, according to comments posted by other people, this problem is not resolved in gatk 4, so gatk 4 cannot do "Split'N'Trim" and I have to use gatk 3.

    Even though you say that I do not need to set those parameters in gatk 4, I find that it works in gatk 3 as well if those parameters are not set at all. This means that both gatk 3 and gatk 4 work without setting those parameters. However, the pipeline requires those parameters to be set in gatk 3 (and maybe in gatk 4 as well). Thus, I am a bit uncertain about whether it is correct to do Split'N'Trim without setting those parameters (i.e. reassign mapping qualities) using gatk 4. Is it okay to do Split'N'Trim using gatk 4 without being able to set those parameters for reassigning mapping qualities?

    Thanks.

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @XiaoshenYin

    One of the changes in gatk4 was to remove options from gatk3 that were redundant. And as you mentioned: > you find that it works in gatk 3 as well if those parameters are not set at all.
    Hence, i suggested you do not need to set those two parameters.
    You could test this out for yourself by comparing results of a) gatk with those options, b) gatk3 without those options c) gatk4 without those options, while keeping all other options constant. Try this and I would be curious to know what you find.

    Regards
    Bhanu

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