GATK RUNTIME ERROR during AnalyzeCovariates

kjclowerskjclowers UW MadisonPosts: 14Member

I am getting the following error while trying to recalibrate base quality scores at the AnalyzeCovariates step:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.R.RScriptExecutorException: RScript exited with 1. Run with -l DEBUG for more info. at org.broadinstitute.sting.utils.R.RScriptExecutor.exec(RScriptExecutor.java:174) at org.broadinstitute.sting.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:550) at org.broadinstitute.sting.gatk.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:380) at org.broadinstitute.sting.gatk.walkers.bqsr.AnalyzeCovariates.initialize(AnalyzeCovariates.java:394) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.6-5-gba531bd):
ERROR
ERROR Please check the documentation guide to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: RScript exited with 1. Run with -l DEBUG for more info.
ERROR ------------------------------------------------------------------------------------------

Thanks, Katie

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