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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

GATK not responding after STATUSLogger Error

I am trying to determine the coverage depth for the given BAM files using GATK (version 3.8). The reason of using older version of GATK is that I do not find any such tool in GATK4. Initially gatk3 was throwing error due to java compatibility issues because of jdk version 10 and then solved with jdk-8 (locally installed). After that now it is throwing a different error (as shown below) and it is just hangs there and not responding anything. Please see the error message below:

Run GATK for depth of coverage of group1....
INFO 11:18:29,148 HelpFormatter - ----------------------------------------------------------------------------------
INFO 11:18:29,151 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 11:18:29,152 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 11:18:29,152 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 11:18:29,152 HelpFormatter - [Fri Dec 14 11:18:29 IST 2018] Executing on Linux 4.15.0-36-generic amd64
INFO 11:18:29,152 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_191-b12
INFO 11:18:29,156 HelpFormatter - Program Args: -T DepthOfCoverage -I /home/vivekr /cnv_xhmm/group1.READS.bam.list -L /home/vivekr/cnv_xhmm/final.interval_list -R /home/vivekr/cnv_xhmm/HiSeqAnalysisSoftware_UCSC_hg19/Sequence/IsaacIndex/genome.fa -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o /home/vivekr/cnv_xhmm/group1.DATA
INFO 11:18:29,157 HelpFormatter - Executing as [email protected] on Linux 4.15.0-36-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_191-b12.
INFO 11:18:29,157 HelpFormatter - Date/Time: 2018/12/14 11:18:29
INFO 11:18:29,157 HelpFormatter - ----------------------------------------------------------------------------------
INFO 11:18:29,158 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/home/vivekr/Packages/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...


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