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Hi there, I've tried to run ReduceReads for the first time and I got this error:

`$ java -Xmx8g -jar /lustre1/tools/bin/GenomeAnalysisTK-2.3-6.jar -T ReduceReads -R /lustre1/genomes/hg19/fa/hg19.fa -I filein.bam -o fileout.bam […]

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

ERROR stack trace

java.lang.NullPointerException 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:91)

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

ERROR A GATK RUNTIME ERROR has occurred (version 2.3-6-gebbba25):

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 ------------------------------------------------------------------------------------------

` Is there something wrong with running RR with multiple samples?

d

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