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lanagarmire / SSrGE

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A USER ERROR has occurred (version 3.8-0-ge9d806836): #11

Open elbakrifz opened 4 years ago

elbakrifz commented 4 years ago

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 commented 4 years ago

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

lanagarmire commented 4 years ago

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