Error related to log4j2 (with gatk `v3.8.0`)

[Mxrcon]

I'm trying to run the pipeline on a PBS cluster and during the TBBWA step, I'm getting this very odd error:

ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/laboratorio/sabmi/karla.lima/sabmi_sra_marilia/mtbseq_nf_test/mtbseq-nf/conda_envs/mtbseq-nf-env/opt/gatk-3.8/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  16:18:38,339 GenomeAnalysisEngine - Deflater: JdkDeflater 
INFO  16:18:38,340 GenomeAnalysisEngine - Inflater: JdkInflater 
INFO  16:18:38,341 GenomeAnalysisEngine - Strictness is SILENT 
INFO  16:18:38,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 10000 
INFO  16:18:38,510 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  16:18:38,587 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07 
##### ERROR ------------------------------------------------------------------------------------------

I'm using a new conda environtment provided by the recipe on this repository, I'm also using the correct GATK jar.

[abhi18av]

This seems related https://github.com/ngs-fzb/MTBseq_source/issues/23 and reported for a conda_env, which I haven't been able to reproduce on my setup yet.

Note that I haven't been able to reproduce this issue using the docker container, either.

I can't agree with classifying this as a bug since this relates to an underlying tool, which we happen to use i.e. gatk, maybe it should be called known_issue.

[Mxrcon]

I'm testing the GATKjar version 3.8.1 (GenomeAnalysisTK-3.8-1-0-gf15c1c3ef), avaible on this link: https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2

As suggested on this issue, so we can see if updating the jar solves the problem with mtbseq

[Mxrcon]

After a long test on IEC Cluster the issue seems to be fixed, If it's okay to you @abhi18av, I'll close this issue and keep it as a possible troubleshooting for future use.

[abhi18av]

Brilliant!

@Mxrcon , would you mind adding a general outline of the solution please?

[Mxrcon]

Sure!

• [ ] Download a new GATK tar

wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2

• [ ] Untar the GATK.jar

  tar -xvf GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2

• [ ] Register the new GATK and use on the pipeline as usual

  gatk-register GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar

[abhi18av]

Hmm, I see.

In that case, do you think it's worth upgrading the default gatk version within the pipeline?

I have updated the title of this issue to help anyone discover the cause of this issue earlier.