When will AnalyzeCovariates support R/4.0
Hi
Seems GATK4 (AnalyzeCovariates) use Rscript but not support R/4.0 yet. I solved the problem by loading R/3.6.3 instead, I think it's worth to share.
Can you please provide
a) GATK version used : GATK 4.1.7.0
b) Exact GATK commands used :
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms100G -jar /usr/local/apps/GATK/4.1.4.1/gatk-package-4.1.4.1-local.jar AnalyzeCovariates -bqsr WPS_21.recalibrated.bam_rbqsr.report -plots test.pdf
c) The entire error log if applicable.
Error in distributeGraphRows(list(a, b, c), c(1, 1, 1)) :
object 'a' not found
Calls: source -> withVisible -> eval -> eval -> distributeGraphRows
Execution halted
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:126)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:126)
at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:360)
at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:329)
at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.doWork(AnalyzeCovariates.java:341)
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)
-
Hi Qi Yu
Thanks for the update. This will help other GATK users too!
Please sign in to leave a comment.
1 comment