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No plots generated by the BaseRecalibrator walker

I cannot produce BQSR plots, although I can open the grp file with gsa.read.gatkreport.

Here's the command:

java -Xmx1g -jar $shares/GenomeAnalysisTK-2.3-6-gebbba25/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -I ./0.reorder.bam \ -R $shares/ftp.broadinstitute.org/bundle/2.3/hg19/ucsc.hg19.fasta \ -knownSites $shares/ftp.broadinstitute.org/bundle/2.3/hg19/dbsnp_137.hg19.vcf \ -BQSR ./0.reorder.bam.recal.grp \ -o ./0.reorder.bam.post_recal.grp \ --plot_pdf_file ./0.reorder.bam.post_recal.grp.pdf \ -L chr1:1-1000 \ -l DEBUG \ --intermediate_csv_file ./0.reorder.bam.post_recal.grp.csv

##### ERROR stack trace java.lang.NullPointerException at org.broadinstitute.sting.utils.Utils.join(Utils.java:286) at org.broadinstitute.sting.utils.recalibration.RecalUtils.writeCSV(RecalUtils.java:450) at org.broadinstitute.sting.utils.recalibration.RecalUtils.generateRecalibrationPlot(RecalUtils.java:394) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.generatePlots(BaseRecalibrator.java:474) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:464) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:112) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:97) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

It looks like the csv file is not being produced.

Thanks!

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Alright, what's failing is the method that creates the data lines to be written to the csv file. It's an extremely simple operation so there's got to be something wrong with your data. Considering the interval that you're running on is extremely short, there may not even be any valid data at all in the part of the table that fails to write. You should try running again from the first step of recalibration with a much longer interval, eg 20:10000000-20000000.

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