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GATK 4 VariantRecalibrator throws error for missing R path, but only for SNPs

oskarvoskarv BergenMember
edited August 2017 in Ask the GATK team

I'm not using the --rscript_file option, but VariantRecalibrator for SNPs still throws an error for it, but it's fine with the exact same command, except -mG 4, in the INDEL run. And it produces the output just fine, but for some reason complains about not finding Rscript.

Here's the stderr output of the SNP run, edited for readability.

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=call-VariantRecalibratorSNP/execution/tmp.sAdeNd
[August 9, 2017 6:36:15 AM UTC] VariantRecalibrator  --mode SNP --resource v1000G:1000G_phase1.snps.high_confidence.hg38.vcf.gz --resource omni:1000G_omni2.5.hg38.vcf.gz --resource dbsnp:dbsnp_146.hg38.vcf.gz --resource hapmap:hapmap_3.3.hg38.vcf.gz --output GVCF.varRec.SNP.recal --tranches_file GVCF.varRec.SNP.tranches --use_annotation QD --use_annotation MQ --use_annotation DP --use_annotation MQRankSum --use_annotation ReadPosRankSum --use_annotation FS --use_annotation SOR --TStranche 100.0 --TStranche 99.95 --TStranche 99.9 --TStranche 99.8 --TStranche 99.6 --TStranche 99.5 --TStranche 99.4 --TStranche 99.3 --TStranche 99.0 --TStranche 98.0 --TStranche 97.0 --TStranche 90.0 --variant GVCF.genotypegvcf.g.vcf --reference Homo_sapiens_assembly38.fasta  --useAlleleSpecificAnnotations false --maxGaussians 8 --maxNegativeGaussians 2 --maxIterations 150 --numKMeans 100 --stdThreshold 10.0 --shrinkage 1.0 --dirichlet 0.001 --priorCounts 20.0 --maxNumTrainingData 2500000 --minNumBadVariants 1000 --badLodCutoff -5.0 --MQCapForLogitJitterTransform 0 --no_MQ_logit false --MQ_jitter 0.05 --target_titv 2.15 --ignore_all_filters false --sample_every_Nth_variant 1 --output_tranches_for_scatter false --replicate 200 --max_attempts 1 --trustAllPolymorphic false --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --readValidationStringency SILENT --secondsBetweenProgressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --createOutputBamMD5 false --createOutputVariantIndex true --createOutputVariantMD5 false --lenient false --addOutputSAMProgramRecord true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disableBamIndexCaching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --disableToolDefaultReadFilters false
[August 9, 2017 6:36:15 AM UTC] Executing as [email protected] on Linux 2.6.32-642.11.1.el6.centos.plus.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11; Version: 4.beta.3
[August 9, 2017 7:13:35 AM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 37.34 minutes.
Runtime.totalMemory()=5059379200
***********************************************************************

A USER ERROR has occurred: Unable to execute RScript command: Please add the Rscript directory to your environment ${PATH}

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--javaOptions '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

And the INDEL stderr.

[August 9, 2017 6:36:15 AM UTC] VariantRecalibrator  --mode INDEL --maxGaussians 4 --resource mills:Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --resource dbsnp:dbsnp_146.hg38.vcf.gz --output GVCF.varRec.INDEL.recal --tranches_file GVCF.varRec.INDEL.tranches --use_annotation QD --use_annotation DP --use_annotation FS --use_annotation SOR --use_annotation ReadPosRankSum --use_annotation MQRankSum --TStranche 100.0 --TStranche 99.95 --TStranche 99.9 --TStranche 99.5 --TStranche 99.0 --TStranche 97.0 --TStranche 96.0 --TStranche 95.0 --TStranche 94.0 --TStranche 93.5 --TStranche 93.0 --TStranche 92.0 --TStranche 91.0 --TStranche 90.0 --variant GVCF.genotypegvcf.g.vcf --reference Homo_sapiens_assembly38.fasta  --useAlleleSpecificAnnotations false --maxNegativeGaussians 2 --maxIterations 150 --numKMeans 100 --stdThreshold 10.0 --shrinkage 1.0 --dirichlet 0.001 --priorCounts 20.0 --maxNumTrainingData 2500000 --minNumBadVariants 1000 --badLodCutoff -5.0 --MQCapForLogitJitterTransform 0 --no_MQ_logit false --MQ_jitter 0.05 --target_titv 2.15 --ignore_all_filters false --sample_every_Nth_variant 1 --output_tranches_for_scatter false --replicate 200 --max_attempts 1 --trustAllPolymorphic false --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --readValidationStringency SILENT --secondsBetweenProgressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --createOutputBamMD5 false --createOutputVariantIndex true --createOutputVariantMD5 false --lenient false --addOutputSAMProgramRecord true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disableBamIndexCaching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --disableToolDefaultReadFilters false
[August 9, 2017 6:36:15 AM UTC] Executing as [email protected] on Linux 2.6.32-642.11.1.el6.centos.plus.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11; Version: 4.beta.3
[August 9, 2017 6:52:54 AM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 16.66 minutes.
Runtime.totalMemory()=7318011904

The only occurrence of anything related to R is in the error message, so I don't understand why it's complaining. I run it with cromwell-28_2 and the gatk4 beta 3, and if I run ApplyVQSR with the SNP recal and tranches files it works just fine, so there's nothing wrong with the output files, it's just that it for some reason complains that R is missing even though it's not supposed to try to use R. What could be wrong?

Issue · Github
by Sheila

Issue Number
2429
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

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