BaseRecalibration: Recalibration table is empty
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Comments (39)

When running GATK, I am getting "empty" results when running BaseRecalibrator. I didn't see a solution to this when searching.

java -Xmx4g -jar /seqprg/GenomeAnalysisTK-2.4-3-g2a7af43/GenomeAnalysisTK.jar -l INFO -R /Users/bcantarel/projects/refdb/human_g1k_v37.fasta --knownSites /Users/bcantarel/projects/refdb/00-All.vcf -I Sample_cDNA405.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o Sample_cDNA405.grp

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalStateException: recalibration tables list is empty at org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationEngine.mergeThreadLocalRecalibrationTables(RecalibrationEngine.java:209) at org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationEngine.finalizeData(RecalibrationEngine.java:175) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:508) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:131) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:123) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-3-g2a7af43):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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: recalibration tables list is empty
ERROR ------------------------------------------------------------------------------------------

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