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Select Variants bug

Hi I'm using select variants to extract out variants with PASS filter, and those that are biallelic SNPs with the command below using gatk 3.2-2.

java -Xmx${MEM} -jar ${gatk_dir}/GenomeAnalysisTK.jar -R ${ref_dir}/${genome} \
-T SelectVariants \
--variant "1_"${VCF_FILE}"excCpGRepeat.vcf" \
-ef \
-L $CHROM \
--restrictAllelesTo BIALLELIC \
-selectType SNP \
-o "2
"${VCF_FILE}"_PASSBiSNP_excCpGRepeat.vcf"

I split my vcf using snpsift - so I run it on each chromosome seperately. For 12 of the 38 chromosomes I get the error - the others work fine. I re-extracted one of the chromosomes that failed, to be sure it wasn't a snpsift issue, and it still fails.
Any ideas on what the problem might be?

INFO 15:26:17,318 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:26:17,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 15:26:17,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:26:17,323 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:26:17,328 HelpFormatter - Program Args: -R /u/home/c/projectdata/c/canids/reference/canfam31/canfam31_chr1NOTchr01/canfam31_chr1NOTchr01.fa -T SelectVariants --variant 1.chr35_excCpGRepeat.vcf -ef -L chr35 --restrictAllelesTo BIALLELIC -selectType SNP -o 2_chr35_PASSBiSNP_excCpGRepeat.vcf
INFO 15:26:17,338 HelpFormatter - Executing as @n263 on Linux 2.6.32-431.20.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_55-mockbuild_2014_04_16_12_11-b00.
INFO 15:26:17,338 HelpFormatter - Date/Time: 2014/11/20 15:26:17
INFO 15:26:17,339 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:26:17,339 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:26:17,469 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:26:17,715 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:26:19,240 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:336)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:320)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:279)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:225)
at org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:148)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.(ReferenceOrderedDataSource.java:208)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.(ReferenceOrderedDataSource.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:990)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:772)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:285)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
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)
... 14 more
Caused by: java.io.EOFException
at htsjdk.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:138)
at htsjdk.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:80)
at htsjdk.tribble.index.linear.LinearIndex$ChrIndex.read(LinearIndex.java:271)
at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:363)
at htsjdk.tribble.index.linear.LinearIndex.(LinearIndex.java:101)
... 19 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
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 ------------------------------------------------------------------------------------------

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