The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

Could not find walker with name: "RealignerTargetCreator" and "BaseRecalibrator"

Please find the below code and the error I am getting. I tried all the versions 3.4 to 3.8.1 but I couldn't figure it out. The same error is happening with "BaseRecalibrator " as well, Please let me know the resolution for this problem.

[email protected]:~/Satish$ java -Xmx4g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -o Exome_sample_RG_index.marked.bam.list -I Exome_sample_RG_index.marked.bam -known dbsnp_138.hg19.vcf -L nexterarapidcapture_expandedexome_targetedregions.bed

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
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
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: Malformed walker argument: Could not find walker with name: RealignerTargetCreator


Sign In or Register to comment.