Analyze Covariates nullpointerexception

Hi,

I'm encountering the following error using GATK 2.7-2 and 2.8-1 on R 3.0.2 and sun-java7 on a 64bit system.

I try to generate the pdf plots of BQSR after two rounds of BQSR analysis. The command is :

/opt/software/sun-jre-7/bin/java '-Djava.io.tmpdir=/tmp' '-Xmx4g' '-jar' '/galaxy/scattergather/binaries/gatk/2.8-1-g932cd3a/bin/GenomeAnalysisTK.jar' -l DEBUG '-after' '/galaxy/scattergather/Data_Exomes/131129_SNL167_0056_AC2TLPACXX/105726.after.recal.grp' '-plots' '/galaxy/scattergather/Data_Exomes/131129_SNL167_0056_AC2TLPACXX/105726.BQSR.pdf' '-T' 'AnalyzeCovariates' '-dt' 'NONE' '-R' '/galaxy/scattergather/References/hg19/samtools/0.1.19/hg19.fasta' '-L' '/galaxy/scattergather/Data_Exomes/131129_SNL167_0056_AC2TLPACXX/Targets.extended.bed' '-before' '/galaxy/scattergather/Data_Exomes/131129_SNL167_0056_AC2TLPACXX/105726.recal.grp'

Data is single sample, mapped with 'bwa mem' and processed according to best practice (dedup, real, recal). I also have all the R libraries loaded in BQSR.R

the stack trace:

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

java.lang.NullPointerException
at org.broadinstitute.sting.utils.Utils.join(Utils.java:275)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.writeCSV(RecalUtils.java:638)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.access$100(RecalUtils.java:86)
at org.broadinstitute.sting.utils.recalibration.RecalUtils$CsvPrinter.print(RecalUtils.java:277)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.writeCsv(RecalUtils.java:363)
at org.broadinstitute.sting.utils.recalibration.RecalUtils.generateCsv(RecalUtils.java:344)
at org.broadinstitute.sting.gatk.walkers.bqsr.AnalyzeCovariates.generateCsvFile(AnalyzeCovariates.java:414)
at org.broadinstitute.sting.gatk.walkers.bqsr.AnalyzeCovariates.initialize(AnalyzeCovariates.java:392)
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 2.8-1-g932cd3a):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Any help on resolving this is welcome !

Best,

Geert

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Geert,

    Hm, this sounds like an issue with a missing table. Could you please upload your grp files and the intervals list, so we can debug locally? And can you post the commands that you used for the rounds of BQSR?

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