REQUIRED for all errors and issues:
a) GATK version used:GenomeAnalysisTK-3.5/ 
b) Exact command used: for i in group*.list ; do group=$(echo $i | cut -f1 -d.) ; echo -e '#!'/bin/sh'\n'java -Djava.io.tmpdir=/scr1/users/ostbergk/ -Xmx32g -Xms16g -jar {pipelinepath}gatk/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -et NO_ET  -T DepthOfCoverage -R {referencepath}/reference/Human/human_g1k_v37_decoy.fasta -o ${group}_DoC -I $i -L {referencepath}/Targets/Twist_WES_RefSeq/Twist_WES_RefSeq.bed -ct 20 > ${group}_GATK.sh ; done
c) Entire program log: ##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: DepthOfCoverage
##### ERROR ------------------------------------------------------------------------------------------
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