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Error joinin chromosome datasets

I tried to join chromosome datasets for my SNPs data separated in different chromosomes.

input command:
java -Xmx160g -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants -R /nobackup/data7/jose/Medicago_truncatula_genome/JCVI.Medtr.v4.20130313.fasta -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr1_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr2_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr3_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr4_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr5_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr6_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr7_ReadDepthFiltered.vcf -V /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr8_ReadDepthFiltered.vcf -out /nobackup/data7/jose/GBSv1/Msativa_diploids/hapmap/mergedSNPs/myGBSGenos_mergedSNPs_chr1-8_ReadDepthFiltered.vcf -assumeSorted

error message:

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

java.lang.NullPointerException
at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.setIndexSequenceDictionary(IndexingVariantContextWriter.java:178)
at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.close(IndexingVariantContextWriter.java:133)
at htsjdk.variant.variantcontext.writer.VCFWriter.close(VCFWriter.java:210)
at org.broadinstitute.gatk.tools.CatVariants.execute(CatVariants.java:303)
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.tools.CatVariants.main(CatVariants.java:311)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Any help would be appreciated.

Answers

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