java.lang.reflect.InvocationTargetException for Combine Variants

Hello,

I have a number of multiple individual vcf, which are large in size (average ~ 40 gb) and I am trying to combine them into one vcf. However, when I try to CombineVariants, an error message is reported (see below).

I am using this version of GATK: gatk/3.4-0
and this version of java: Java SE Development Kit version 1.7.0_51

Viewing additional questions, I adjusted the amount of heapsize requested via Java from 32 to 124 with a requested memory allotment of 50 and 150gb. I have also created new .idx files for each of the individual vcf files. And I still get the error below.

Any help would be appreciated. Thanks!

The code I am using is this:

java -Djava.io.tmpdir=/scratch/  
-Xmx124g 
-classpath /N/soft/rhel6/picard/picard-tools-1.107/ 
-jar /N/soft/rhel6/gatk/3.4-0/GenomeAnalysisTK.jar 
-R SL2.50all.fa 
-T CombineVariants -nt 32 
--variant input.list 
-o tomato.raw.all.vcf 
-genotypeMergeOptions REQUIRE_UNIQUE

##### ERROR stack trace 
        java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
    at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:335)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:278)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:224)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:147)
    at 
org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createNewResource(ReferenceOrderedDataSource.java:226)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createNewResource(ReferenceOrderedDataSource.java:185)
    at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:84)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
    at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.<init>(RodLocusView.java:82)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.GeneratedConstructorAccessor31.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:185)
    ... 17 more
Caused by: java.lang.OutOfMemoryError: Java heap space
    at htsjdk.tribble.index.interval.IntervalTreeIndex$ChrIndex.read(IntervalTreeIndex.java:206)
    at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:363)
    at htsjdk.tribble.index.interval.IntervalTreeIndex.<init>(IntervalTreeIndex.java:52)
    ... 21 more


##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
##### 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 http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: java.lang.reflect.InvocationTargetException

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