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Haplotype Caller error with 2.4-3

Hi
I am trying to run Haplotype Caller on illumina 100bp PE data using:
java -jar $gatk_dir/GenomeAnalysisTK.jar -R $reference_dir/$reference -T HaplotypeCaller -I $step10_pe12_out -o "11_NGATK_HC_GaTkSNP"$sample_abb"pe12.vcf"

I first tried using GaTK 2.3-9 and got an error “ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?” posted below in full.

Reading the forums led me to believe that perhaps it is a version issue (http://gatkforums.broadinstitute.org/discussion/1750/haplotypecaller-error-with-reducereads-exomes).

I re-ran the same command using the newly released GaTK2.4-3 and now have a different error

ERROR MESSAGE: Reads are too small for use in assembly. (posted below in full)

It’s noteworthy that Unified Genotyper runs fine on these same files. Previous steps on the files were adaptor removal, trimming by quality and length, aligned with BWA, Mark Duplicates, IndelRealignment, Reduce Reads. I have no variant file, so had to skip the recalibration steps advised in GaTk best practices.

Is this a bug or is there something wrong with my commands and files?

Errors in full:

GaTk 2.3-9

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Too many deletions?
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:447)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:396)
at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:392)
at org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage.annotate(DepthOfCoverage.java:56)
at org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation.annotate(InfoFieldAnnotation.java:24)
at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:223)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents(GenotypingEngine.java:196)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:411)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:107)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:285)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:205)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:131)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:28)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
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: Somehow the requested coordinate is not covered by the read. Too many deletions?
ERROR ------------------------------------------------------------------------------------------

GaTk 2.4-3

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

java.lang.IllegalStateException: Reads are too small for use in assembly.
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.DeBruijnAssembler.createDeBruijnGraphs(DeBruijnAssembler.java:139)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.DeBruijnAssembler.runLocalAssembly(DeBruijnAssembler.java:123)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:483)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:132)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:552)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:512)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:244)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:69)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
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: Reads are too small for use in assembly.
ERROR ------------------------------------------------------------------------------------------

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