Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

No plots generated by the BaseRecalibrator walker

alexpensonalexpenson Posts: 4Member

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 Posts: 5,235 admin
    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.

    Geraldine Van der Auwera, PhD

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