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Hi to all
I have a problem in understanding an error output produced by PrintReads tool. This is my command line(the recal.grp file is correctly produced by BaseRecalibrator tool):

java -jar /Archive/Software/GATK2.1-8/GenomeAnalysisTK.jar -T PrintReads -I /Path-to-BAMfile -BQSR /Path-to-recal.grp -o /Path-to-output

The error output is:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.1-8-g5efb575):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: Walker requires a reference but none was provided.
ERROR ------------------------------------------------------------------------------------------

As apparently no further information are available I cannot understand what is the issue.
Thank for the help!


Best Answer


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