Concordance crashed

Dear Gatk team,
I'm trying to compare two vcfs with genotypes for a single sample on two platforms using Concordance (gatk 4.0.1.1). Getting an error, please help:

[[email protected] Concordance]$ /programs/gatk4/gatk --java-options "-Xmx120G" Concordance -R ../RemapWGS/Reference/v2.refseq/GRCh38_latest_genomic.fna --evaluation qmd-27-07.deep-wes.grch38-refseq.gatk4.qchip-sites.vcf --truth qmd-27-07.deep-wgs.grch38-refseq.gatk4.qchip-sites.vcf --summary concordance.qmd-27-07.eval-deep-wes.truth-deep-wgs.tsv
Using GATK jar /programs/gatk-4.0.1.1/gatk-package-4.0.1.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Xmx120G -jar /programs/gatk-4.0.1.1/gatk-package-4.0.1.1-local.jar Concordance -R ../RemapWGS/Reference/v2.refseq/GRCh38_latest_genomic.fna --evaluation qmd-27-07.deep-wes.grch38-refseq.gatk4.qchip-sites.vcf --truth qmd-27-07.deep-wgs.grch38-refseq.gatk4.qchip-sites.vcf --summary concordance.qmd-27-07.eval-deep-wes.truth-deep-wgs.tsv
14:29:40.034 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/programs/gatk-4.0.1.1/gatk-package-4.0.1.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:29:40.157 INFO Concordance - ------------------------------------------------------------
14:29:40.157 INFO Concordance - The Genome Analysis Toolkit (GATK) v4.0.1.1
14:29:40.157 INFO Concordance - For support and documentation go to https://software.broadinstitute.org/gatk/
14:29:40.158 INFO Concordance - Executing as [email protected] on Linux v3.10.0-693.el7.x86_64 amd64
14:29:40.158 INFO Concordance - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_131-b12
14:29:40.158 INFO Concordance - Start Date/Time: January 8, 2019 2:29:40 PM EST
14:29:40.158 INFO Concordance - ------------------------------------------------------------
14:29:40.159 INFO Concordance - ------------------------------------------------------------
14:29:40.159 INFO Concordance - HTSJDK Version: 2.14.1
14:29:40.159 INFO Concordance - Picard Version: 2.17.2
14:29:40.159 INFO Concordance - HTSJDK Defaults.COMPRESSION_LEVEL : 1
14:29:40.159 INFO Concordance - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:29:40.159 INFO Concordance - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:29:40.159 INFO Concordance - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:29:40.160 INFO Concordance - Deflater: IntelDeflater
14:29:40.160 INFO Concordance - Inflater: IntelInflater
14:29:40.160 INFO Concordance - GCS max retries/reopens: 20
14:29:40.160 INFO Concordance - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
14:29:40.160 INFO Concordance - Initializing engine
14:29:40.712 INFO FeatureManager - Using codec VCFCodec to read file file:///local/storage/AnalysisData/Ongoing/Qatar/Array/QChip/QChipData/v4/GRCh38/Concordance/qmd-27-07.deep-wgs.grch38-refseq.gatk4.qchip-sites.vcf
14:29:40.736 INFO FeatureManager - Using codec VCFCodec to read file file:///local/storage/AnalysisData/Ongoing/Qatar/Array/QChip/QChipData/v4/GRCh38/Concordance/qmd-27-07.deep-wes.grch38-refseq.gatk4.qchip-sites.vcf
14:29:40.744 INFO Concordance - Done initializing engine
14:29:40.745 INFO ProgressMeter - Starting traversal
14:29:40.745 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
14:29:40.958 INFO Concordance - Shutting down engine
[January 8, 2019 2:29:40 PM EST] org.broadinstitute.hellbender.tools.walkers.validation.Concordance done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2092433408
java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at htsjdk.variant.variantcontext.VariantContext.getAlternateAllele(VariantContext.java:879)
at org.broadinstitute.hellbender.tools.walkers.validation.Concordance.areVariantsAtSameLocusConcordant(Concordance.java:256)
at org.broadinstitute.hellbender.engine.AbstractConcordanceWalker$ConcordanceIterator.next(AbstractConcordanceWalker.java:188)
at org.broadinstitute.hellbender.engine.AbstractConcordanceWalker$ConcordanceIterator.next(AbstractConcordanceWalker.java:163)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.traverse(AbstractConcordanceWalker.java:121)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
at org.broadinstitute.hellbender.Main.main(Main.java:277)

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