Hi there, I'm trying to get AnalyzeCovariates to work, and I get the following error message...any thoughts as to what is going wrong? Not sure whether this is a program-related issue or not?
Thanks!!
docsmb17:No_Backup sgfriede$ java -jar /Users/sgfriede/GeneApps/GenomeAnalysisTK-3.1.1/GenomeAnalysisTK.jar -T AnalyzeCovariates \ -R canFam3.fa \ -before recal.table \ -after after_recal.table \ -plots Mariah_recal_plots.pdf
INFO 09:00:35,945 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:00:35,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21
INFO 09:00:35,947 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:00:35,948 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:00:35,951 HelpFormatter - Program Args: -T AnalyzeCovariates -R canFam3.fa -before recal.table -after after_recal.table -plots Mariah_recal_plots.pdf
INFO 09:00:36,278 HelpFormatter - Executing as sgfriede@docsmb17.local on Mac OS X 10.9.3 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_55-b13.
INFO 09:00:36,279 HelpFormatter - Date/Time: 2014/05/26 09:00:35
INFO 09:00:36,279 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:00:36,279 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:00:36,706 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:00:37,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:00:37,163 GenomeAnalysisEngine - Preparing for traversal
INFO 09:00:37,179 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:00:37,179 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:00:37,179 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 09:00:37,514 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 09:00:37,802 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 09:00:37,852 AnalyzeCovariates - Generating csv file '/var/folders/jx/3t4ylccn0g32xwl0qs6y4tz80000gp/T/AnalyzeCovariates3417596129729096429.csv'
INFO 09:00:38,256 AnalyzeCovariates - Generating plots file 'Mariah_recal_plots.pdf'
INFO 09:00:39,706 GATKRunReport - Uploaded run statistics report to AWS S3
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:548)
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:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)