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Hi,

when I run ReduceReads I get the following exception just when it's supposed to finish:

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.util.NoSuchElementException at java.util.LinkedList$ListItr.next(Unknown Source) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.updateHeaderCounts(SlidingWindow.java:697) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SlidingWindow.addRead(SlidingWindow.java:128) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.addAlignment(SingleSampleCompressor.java:73) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:70) 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:347) at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:86) at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:107) at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:52) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:71) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269) 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 2.0-21-ga40b695):

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: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------

I run it with the standard arguments: java -jar GenomAnalysisTK.jar \ --logging_level ERROR \ -R hg19.fa \ -T ReduceReads \ -I in.bam \ -o reduced.in.bam

Anny suggestions?

Thanks, Thomas

There are 27 comments on this article. To see them or add your own, view this post on the forum