Tagged with #reviewedstingexception
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Comments (23)

New gatk version... trying out ReduceReads again.

6 of 8 exomes I tried were processed by ReduceReads just fine, but two throw the exception Removed too many insertions, header is now negative! (at different genomic locations).

I did not find any mention of this error in the GATK forums, is this a known problem?

Command line: java -Xmx6g -jar GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T ReduceReads -o test.rr.bam -I rr-too-many-insertions.bam

java -v: java version "1.6.0_27" Java(TM) SE Runtime Environment (build 1.6.0_27-b07) Java HotSpot(TM) 64-Bit Server VM (build 20.2-b06, mixed mode)

Run log:

INFO  16:03:26,898 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  16:03:27,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-0-g9593e74, Compiled 2012/12/17 16:58:19 
INFO  16:03:27,383 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  16:03:27,383 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  16:03:27,388 HelpFormatter - Program Args: -R human_g1k_v37.fasta -T ReduceReads -o test.rr.bam -I rr-too-many-insertions.bam 
INFO  16:03:27,388 HelpFormatter - Date/Time: 2012/12/18 16:03:26 
INFO  16:03:27,388 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  16:03:27,388 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  16:03:27,471 GenomeAnalysisEngine - Strictness is SILENT 
INFO  16:03:27,577 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  16:03:27,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  16:03:27,620 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 
INFO  16:03:27,656 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  16:03:27,657 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
INFO  16:03:27,714 ReadShardBalancer$1 - Loading BAM index data for next contig 
INFO  16:03:27,717 ReadShardBalancer$1 - Done loading BAM index data for next contig 
INFO  16:03:27,739 ReadShardBalancer$1 - Loading BAM index data for next contig 
INFO  16:03:28,739 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Removed too many insertions, header is now negative!
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.HeaderElement.removeInsertionToTheRight(HeaderElement.java:151)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.updateHeaderCounts(SlidingWindow.java:881)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.removeFromHeader(SlidingWindow.java:816)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.compressVariantRegion(SlidingWindow.java:604)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:623)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:643)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.closeVariantRegions(SingleSampleCompressor.java:83)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.closeVariantRegionsInAllSamples(MultiSampleCompressor.java:94)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:76)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:387)
    at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:87)
    at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:226)
    at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:215)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:254)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
    at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
    at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
    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:94)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-0-g9593e74):
##### 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: Removed too many insertions, header is now negative!
##### ERROR ------------------------------------------------------------------------------------------

(there is no progress listed here because this log is from after I bisected to find a narrow region where the problem is occuring).

Comments (33)

Hello dear GATK Team,

when trying to run Haplotypecaller on my exome files prepared with ReduceReads i get the error stated below. As you can see the newest GATK Version is used. Also UnifiedGenotyper does not produce any errors on te exact same data (90 SOLiD exomes creatted according to Best Practice v4).

##### 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.HaplotypeCaller.map(HaplotypeCaller.java:429)
    at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:104)
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:249)
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:204)
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:179)
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:136)
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:29)
    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:236)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-3-gde33222):
##### 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 ------------------------------------------------------------------------------------------

The Command line used (abbreviated):

java -Xmx30g -jar /home/common/GenomeAnalysisTK-2.2-3/GenomeAnalysisTK.jar \
  -R /home/common/hg19/ucschg19/ucsc.hg19.fasta \
  -T HaplotypeCaller \
  -I ReduceReads/XXXXX.ontarget.MarkDups.nRG.reor.Real.Recal.reduced.bam [x90]\
  --dbsnp /home/common/hg19/dbsnp_135.hg19.vcf \
  -o 93Ind_ped_reduced_HC_snps.raw.vcf \
  -ped familys.ped \
  --pedigreeValidationType SILENT \
  -stand_call_conf 20.0 \
  -stand_emit_conf 10.0