GATK R plots with R v4.1.2

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Franz Gassner

• January 24, 2022 09:36

Hello,

I have R v 4.1.2 installed on my RedHat system. both R and GATK are in PATH. Default R library location is /home/m3fga/R/x86_64-redhat-linux-gnu-library/4.1

In R, the "optparse" package is installed. However, with "PlotDenoisedCopyRatios" I get the error as described below. (same error for "PlotModeledSegments")

Do I need a specific R version for "PlotDenoisedCopyRatios"?
Do I need a specific library location for GATK to find the libraries? (plotting_dump.rda suggests /opt/R/3.6.3/lib/R/library, but copying the libraries there had no effect)

Can I modify GATK to use a different R version and/or look for packages in a different location?

Many thanks in advance!

best,

Franz

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.3.0
b) Exact command used: gatk PlotDenoisedCopyRatios --denoised-copy-ratios 02_copy_ratios/${patients[$i]}"_CLL.denoisedCR.tsv" --standardized-copy-ratios 02_copy_ratios/${patients[$i]}"_CLL.standardizedCR.tsv" --sequence-dictionary ~/limcr-ngs/databases/hg38/hg38.dict -O 05_plots --output-prefix ${patients[$i]}
c) Entire error log: Stderr: Error in library(optparse) : there is no package called ‘optparse’
Calls: source -> withVisible -> eval -> eval -> library

at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:80)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:19)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:130)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:126)
at org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios.writeDenoisingPlots(PlotDenoisedCopyRatios.java:223)
at org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios.doWork(PlotDenoisedCopyRatios.java:172)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)

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• 

  Genevieve Brandt (she/her)

  • January 24, 2022 20:23

  Hi Franz Gassner,

  Information about the R tool versions can be found in the tutorial (How to part I) Sensitively detect copy ratio alterations and allelic segments, in the section 'Tools Involved'. I highly recommend using gatk with Docker when you are trying to use these tools. In the GATK Docker container, you won't have to worry about the installation of all the specific R tools. 

  Here is a helpful article: (How to) Run GATK in a Docker container. 

  Let me know if you have further questions.

  Best,

  Genevieve

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  Franz Gassner

  • January 25, 2022 08:16

  Hi Genevieve,

  Using Docker and the article you linked worked perfectly.

  Thank you!

  Best,

  Franz

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  Genevieve Brandt (she/her)

  • January 25, 2022 17:22

  Great to hear, thanks for the update!

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