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MuTect2 not found using GATK version 3.8 and Java 1.8


I receive an error of not finding MuTect2 when trying to run it with GATK version 3.8 and Java 1.8. Please, find below the Java version:
java version "1.8.0_112"
Java(TM) SE Runtime Environment (build 1.8.0_112-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)

The error message:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836):
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 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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Invalid command line: Multiple values associated with given definition, but this argument expects only one: analysis_type
ERROR ------------------------------------------------------------------------------------------

And this was the call that I made:
java -Xmx512g -jar ${GATK_TO_USE} -T MuTect2 -R $ReferenceGenome -I:normal $MuTect21I -T:tumor $MuTect22I -ploidy 2 --max_alt_alleles_in_normal_count 5 --min_base_quality_score 20 -o $Mutect2O

Am I missing something here, I understood that Java 1.8 is required for GATK 3.8 and MuTect2 should be included in the GATK version? Could you please help?

best regards,



Best Answer


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