RealignerTargetCreator -L parameter error

Hi
I am using the RealignerTargetCreator tool with the -L parameter on whole genome seq. I have about 670000 regions in my BED file and I am getting the following error:

##### ERROR --
##### ERROR stack trace 
java.lang.NullPointerException
    at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
    at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
    at java.util.Arrays.sort(Arrays.java:1312)
    at java.util.Arrays.sort(Arrays.java:1506)
    at java.util.ArrayList.sort(ArrayList.java:1454)
    at java.util.Collections.sort(Collections.java:141)
    at org.broadinstitute.gatk.utils.interval.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:255)
    at org.broadinstitute.gatk.utils.interval.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:872)
    at org.broadinstitute.gatk.utils.interval.IntervalUtils.loadIntervals(IntervalUtils.java:679)
    at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalBindingsPair(IntervalUtils.java:656)
    at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:616)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:774)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:285)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

what does it mean?

with fewer regions it's work fine..

thanks

Omri

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