Base Recalibration plots:RScript exited with 1

Answers

• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  November 2013 Accepted Answer

  You can try to run the BQSR Rscript directly, which will help you troubleshoot. To get the Rscipt, you'll need to get the source code from our github repository here: https://github.com/broadgsa/gatk-protected

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• rb2905 New YorkMember ✭

  November 2013

  The rest of the packages gplots,reshape were missing in R , now the script works from GATK

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  November 2013

  Great, glad to hear it.

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• rb2905 New YorkMember ✭

  November 2013

  HI Geraldine,

  I wanted to know the purpose of the second pass in recalibration ,since its does not recalibrate again but while generating the plots we compare both the recalibration passes.

  The first step is termed "before recalibration" and the second is "after recalibration" but the first step itself is doing recalibration.so why not compare before doing the first pass and after the first pass which recalibrates.

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  November 2013 Accepted Answer

  @rb2905,

  The first step of a recalibration run is the process of calculating the empirical qualities and contrasting them to the existing (reported) qualities in the file, in order to predict what adjustments need to be made. So in order to do the before/after plots, you need to run this on your recalibrated file to find out if the recalibration brought your base qualities closer to reality or not. Make sense?

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• rb2905 New YorkMember ✭

  November 2013

  Yes,it definitely makes sense but the commands listed make a bit hard to understand.
  As,In the second pass we are not doing any recalibration on a recalibrated bam file but just giving the input of the a recalibrated table created in the first pass, to generate a table of post recalibration values

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  November 2013

  Hmm, I see your point. It is actually functionally equivalent to running BaseRecalibrator on the recalibrated file without the BQSR argument. But ideally you should make the plots before generating the recalibrated file, which is why we give this version of the commands. I'll see if I can make this a little clearer in the explanation.

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• rb2905 New YorkMember ✭

  November 2013

  That would be great.
  Thanks again!

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• rb2905 New YorkMember ✭

  November 2013

  The steps mentioned for Base Recalibration are clearer here in this link (Walkthrough of Oct2013 GATK workshop)
  http://www.broadinstitute.org/gatk/guide/topic?name=tutorials

  since in the second pass they use recalibrated bam file(after Print reads) as an input(recalibrated_20.bam) to the second pass.

  java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R human_b37_20.fasta -I realigned_20.bam -knownSites dbsnp_b37_20.vcf -knownSites indels_b37_20.vcf -o recal_20.table -L 20

  java -jar GenomeAnalysisTK.jar -T PrintReads -R human_b37_20.fasta -I realigned_20.bam -BQSR recal_20.table -o recal_20.bam -L 20

  java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R human_b37_20.fasta -I recalibrated_20.bam -knownSites dbsnp_b37_20.vcf -knownSites indels_b37_20.vcf -o post_recal_20.table -L 20

  java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R human_b37_20.fasta -before recal_20.table -after post_recal_20.table -plots recalibration_plots.pdf -L 20

  Thanks,
  Rohan

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• ChrisPatterson Epilepsy Genomics CenterMember ✭

  March 2014

  I'm getting the same error as above, but I'm not clear what you did to fix it exactly. Which R packages does GATK need to run AnalyzeCovariates?

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  March 2014

  The gsalib package from CRAN along with all dependencies (ggplot2, gplot etc).

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• FabriceBesnard ParisMember ✭

  April 2014 edited April 2014

  Hi Geraldine,

  I'm having the same issue:

  I Run:
  java -Xmx4g -jar $GATKDir/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /media/sf_SequencingData/Genomes/Briggsae_Genomes/Cbriggsae_WS238/briggsae.WS238.genome_masked.fa -before HK104_1-recal_data-1.table -after HK104_1-post_recal_data-1.table -plots HK104_1-recalibration_plots1.pdf

  I get the following error message:

  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)

  ERROR ------------------------------------------------------------------------------------------

  ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):

  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: RScript exited with 1. Run with -l DEBUG for more info.

  ERROR ------------------------------------------------------------------------------------------

  I have R installed, as confirmed by running: $ which Rscript, which gives:
  /usr/bin/Rscript

  Within RStudio, I verified the installed packages by running:

  installed.packages()

  And I see, among all the many packages there, with a correct LibPath:

  ggplot2 "/home/fabrice/R/x86_64-pc-linux-gnu-library/3.0"

  gplots "/home/fabrice/R/x86_64-pc-linux-gnu-library/3.0"
  gsalib "/home/fabrice/R/x86_64-pc-linux-gnu-library/3.0"

  Would you know what's going wrong?

  Finally, I don't get what you mean by saying:

  "You can try to run the BQSR Rscript directly"

  Do you mean, within R studio, launching a command with recal_data.table & post_recal_data.table to write the plots ?

  Thank you !
  Fabrice

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  April 2014

  Do you mean, within R studio, launching a command with recal_data.table & post_recal_data.table to write the plots ?

  Yes, exactly that. You will get more immediate information about what's going wrong.

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• FabriceBesnard ParisMember ✭

  April 2014

  Hi,

  Thank you again for your quick reply !
  I went to GitHub at this location: gatk-protected / protected / gatk-protected / src / main / java / org / broadinstitute / sting /
  and look around for the Rscript of "analyze covariates" from BQSR... but I found nothing I expected !

  In gatk-protected / protected / gatk-protected / src / main / java / org / broadinstitute / sting / gatk / walkers / bqsr /,
  but I found only .java files...
  Same thing in: gatk-protected / protected / gatk-protected / src / main / java / org / broadinstitute / sting / utils / recalibration /

  Then, I'm not really sure of what to do with R once I get the script. Tell me if I am wrong:
  -Can I save the script of AnalyzeCovariates anywhere in my computer or somewhere in a dedicated R directory?
  -I start R studio and I source the script using: >source("/path/to/the/Rscript) ?
  -and then? What are the arguments to use? Will the script asked me where my input files are? etc...

  Fabrice

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  April 2014 edited April 2014

  Hi Fabrice, the script you want is here:

  https://github.com/broadgsa/gatk-protected/blob/master/public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R

  You'll need to make AnalyzeCovariates save the intermediate csv script to your working directory using the --intermediateCsvFile argument. The command you need to run should be in the log of your AnalyzeCovariates run; you may need to run with l DEBUG (I forget if it's logged by default).

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• sols saols, manipalMember ✭

  April 2015

  @FabriceBesnard said:
  Hi Geraldine,

  I'm having the same issue:

  I Run:
  java -Xmx4g -jar $GATKDir/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /media/sf_SequencingData/Genomes/Briggsae_Genomes/Cbriggsae_WS238/briggsae.WS238.genome_masked.fa -before HK104_1-recal_data-1.table -after HK104_1-post_recal_data-1.table -plots HK104_1-recalibration_plots1.pdf

  I get the following error message:

  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)

  ERROR ------------------------------------------------------------------------------------------

  ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):

  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: RScript exited with 1. Run with -l DEBUG for more info.

  ERROR ------------------------------------------------------------------------------------------

  I have R installed, as confirmed by running: $ which Rscript, which gives:
  /usr/bin/Rscript

  Within RStudio, I verified the installed packages by running:
  Fabrice

  I had the same problem and installing the R package reshape worked.
  I ran the GTAK command normally after rehape and it worked flawlessly.

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• xcq fuzhouMember ✭

  October 2015

  i cant find BQSR.R on the https://github.com/broadgsa/gatk-protected/blob/master/public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R

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• Sheila Broad InstituteMember, Broadie, Moderator admin

  October 2015

  @xcq
  Hi,

  This article should help: http://gatkforums.broadinstitute.org/discussion/4294/analyzecovariates-fails-with-error-message-rscript-exited-with-1

  -Sheila

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• sonhenson KenyaMember ✭

  September 2016 edited September 2016

  @xcq said:
  i cant find BQSR.R on the https://github.com/broadgsa/gatk-protected/blob/master/public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R

  I found the R script here - https://github.com/broadgsa/gatk-protected/blob/e91472ddc7d58ace52db0cab4d70a072a918d64c/public/gatk-engine/src/main/resources/org/broadinstitute/gatk/engine/recalibration/BQSR.R

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• dbecker MunichMember ✭✭✭

  November 2016

  Why dont't you start your R Scripts with something like that for the required libraries.

  if ( ! "" %in% rownames(installed.packages()) ) {
  install.packages("")
  }

  This might make it more comfortable for some users (myself included). I spend some time reading source code before I found this discussion. But now that I did, it works. Thanks!

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