The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

No plots generated by the BaseRecalibrator walker

alexpensonalexpenson Member Posts: 4

I cannot produce BQSR plots, although I can open the grp file with

Here's the command:

java -Xmx1g -jar $shares/GenomeAnalysisTK-2.3-6-gebbba25/GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-I ./0.reorder.bam \
-R $shares/ \
-knownSites $shares/ \
-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 
        at org.broadinstitute.sting.utils.Utils.join(
        at org.broadinstitute.sting.utils.recalibration.RecalUtils.writeCSV(
        at org.broadinstitute.sting.utils.recalibration.RecalUtils.generateRecalibrationPlot(
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.generatePlots(
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(
        at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(

It looks like the csv file is not being produced.


Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,015 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


Sign In or Register to comment.