Base Recalibration plots:RScript exited with 1
Posted in Ask the team | Last updated on


Comments (15)

I want to create plots before and after Recalibration, and getting the error below:

I have checked for the package "ggplot2"which is required for generating graphs and also added the path of R script to my environment: which is confirmed by :

$ which Rscript

/nfs/apps/R/2.15.1/bin/Rscript

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:313) 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 2.7-4-g6f46d11):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: RScript exited with 1. Run with -l DEBUG for more info.

Below is the command I am running:

/shares/jre1.7.0_40/bin/java -jar /shares/GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /shares/dbdata/human_g1k_v37.fasta -before /shares/bam_base_recalib/recal_data.table -after /shares/bam_base_recalib/post_recal_data.table -plots /shares/bam_base_recalib/BQSR.pdf


Return to top Comment on this article in the forum