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gatk4 error: java.lang.IllegalStateException: The covariates table is missing ReadGroup

LavanyaLavanya Member
edited March 2 in Ask the GATK team

Hi,
Trying to run GATK4 best practice on AWS batch setup with docker (using SSDs).
In most of the time "ApplyBQSR" fails with the following error.

Oops... Pipeline execution stopped with the following message: 08:43:27.126 INFO ApplyBQSR - ------------------------------------------------------------ 08:43:27.126 INFO ApplyBQSR - ------------------------------------------------------------ 08:43:27.126 INFO ApplyBQSR - HTSJDK Version: 2.14.1 08:43:27.126 INFO ApplyBQSR - Picard Version: 2.17.2 08:43:27.126 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 1 08:43:27.126 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 08:43:27.126 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 08:43:27.126 INFO ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 08:43:27.127 INFO ApplyBQSR - Deflater: IntelDeflater 08:43:27.127 INFO ApplyBQSR - Inflater: IntelInflater : 08:43:27.954 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 08:43:28.470 INFO ApplyBQSR - Shutting down engine [February 28, 2018 8:43:28 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2112618496 java.lang.IllegalStateException: The covariates table is missing ReadGroup e5dae369 in RecalTable0 at org.broadinstitute.hellbender.utils.Utils.validate(Utils.java:706) at org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate.keyForReadGroup(ReadGroupCovariate.java:81) at org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate.recordValues(ReadGroupCovariate.java:53) at org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList.recordAllValuesInStorage(StandardCovariateList.java:133) at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.computeCovariates(RecalUtils.java:546) at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.computeCovariates(RecalUtils.java:527) at org.broadinstitute.hellbender.transformers.BQSRReadTransformer.apply(BQSRReadTransformer.java:145) at org.broadinstitute.hellbender.transformers.BQSRReadTransformer.apply(BQSRReadTransformer.java:27) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:94) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:277) Using GATK jar /opt/conda/share/gatk4-4.0.1.1-0/gatk-package-4.0.1.1-local.jar
Rerunning the same step works most of the time. Any suggestions. Thanks.

Post edited by Lavanya on

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