What is this error? and how to resolve it? It is related to generating pdf

ssunkarassunkara IllinoisMember

INFO 13:15:42,730 AnalyzeCovariates - Generating plots file 'LB0003_recal_plots.pdf'

ERROR --
ERROR stack trace

org.broadinstitute.gatk.utils.R.RScriptExecutorException: RScript exited with 1. Run with -l DEBUG for more info.
at org.broadinstitute.gatk.utils.R.RScriptExecutor.exec(RScriptExecutor.java:176)
at org.broadinstitute.gatk.engine.recalibration.RecalUtils.generatePlots(RecalUtils.java:555)
at org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:373)
at org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates.initialize(AnalyzeCovariates.java:387)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: RScript exited with 1. Run with -l DEBUG for more info.
ERROR ------------------------------------------------------------------------------------------

As per my knowledge, the issue is to install four libraries namely ggplot2,gplots, reshape, gsalib.

Am I correct?

If yes where to install these libraries?

below is the command I am running

java -jar ../GenomeAnalysisTK.jar -T AnalyzeCovariates -R ref_Manta.fa -before LB0003_recal_data.2.table -after LB0003_post_recal_data.2.table -plots LB0003_recal_plots.pdf -log LB0003_plots_efile

Answers

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