Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

ReduceReads problem in GATK v2.6-2-ge03a5e9, Compiled 2013/06/20 20:07

ashishashish Oxford, UKPosts: 9Member

Hello, While trying to run ReduceReads on my BAM outputs of PrintReads, using the latest build v2.6-2-ge03a5e9, I get the following error, kindly comment on this error trace:

Command: java -Xmx8g -jar /path/to/my/server/ashish/tools/GenomeAnalysisTK-2.6-2-ge03a5e9/GenomeAnalysisTK.jar -T ReduceReads -R /path/to/my/server/pipeline/lib/hs37d5.fa -I /path/to/my/server/output/bamext.base.recal/41453_TTAGGC_L002_001.bam -o /path/to/my/server/output/bamext.reduced/41453_TTAGGC_L002_001.bam

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Removed too many insertions, header is now negative at position 151039408 at org.broadinstitute.sting.gatk.walkers.compression.reducereads.HeaderElement.removeInsertionToTheRight(HeaderElement.java:210) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.actuallyUpdateHeaderForRead(SlidingWindow.java:1246) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.updateHeaderCounts(SlidingWindow.java:1162) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.removeFromHeader(SlidingWindow.java:1139) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.compressVariantRegion(SlidingWindow.java:742) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegion(SlidingWindow.java:835) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.closeVariantRegions(SlidingWindow.java:884) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.close(SlidingWindow.java:971) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.addAlignment(SingleSampleCompressor.java:113) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:123) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:116) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:477) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:113) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:251) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:240) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311) 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 2.6-2-ge03a5e9):
ERROR
ERROR Please check the documentation guide 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 at position 151039408
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

Sign In or Register to comment.