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- /usr/bin/java -Xmx5G -Xms5G -jar /mnt/f/ANALYSIS_TOOLS/TOOL_BINARIES/gatk/versions/3.7/bin/GenomeAnalysisTK.jar -T MuTect2
- ##### ERROR ------------------------------------------------------------------------------------------
- ##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
- ##### 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 https://software.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: MuTect2
- ##### ERROR ------------------------------------------------------------------------------------------
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