A USER ERROR has occurred (version 3.8-0-ge9d806836):

[elbakrifz]

I was Running this command : java -jar /Users/mac/Downloads/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta -I /Users/mac/Desktop/NGS/ERR439247_sorted.bam -O SRR6369642_realtarget.list
its gave me
A USER ERROR has occurred (version 3.8-0-ge9d806836):

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: RealignerTargetCreator

ERROR ----------------

Please guide me how to overcome this problem
thank you

[elbakrifz]

I downloaded the java version 8 but still have the same error

[lanagarmire]

Please use the docker version since GATK/samtools have updated their API which made them not compatible anymore with the SSRGEpipeline developed at the time. I'm very sorry for the current issue and we are planning to update SSRGE SNVs calling using the new GATK api in a recent future