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Run time error with VariantsToBinaryPed

mcvumcvu IrelandMember

I am trying to covert a vcf file to a bed file using VariantsToBinaryPed. Input: vcf file and metadata file. Error below. Can anyone advise? Thanks!

[[email protected] unag]$ java -jar /data4/una/GenomeAnalysisTK.jar -T VariantsToBinaryPed -R /data4/una/unag/index/human_g1k_v37.fasta -V GTEx.vcf -m GTEx.fam -bed output.bed -bim output.bim -fam output.fam -mgq 0
INFO 10:54:37,479 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:54:37,482 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 10:54:37,482 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 10:54:37,483 HelpFormatter - For support and documentation go to
INFO 10:54:37,483 HelpFormatter - [Tue May 23 10:54:37 BST 2017] Executing on Linux 2.6.18-404.el5 amd64
INFO 10:54:37,483 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13
INFO 10:54:37,490 HelpFormatter - Program Args: -T VariantsToBinaryPed -R /data4/una/unag/index/human_g1k_v37.fasta -V GTEx.vcf -m GTEx.fam -bed output.bed -bim output.bim -fam output.fam -mgq 0
INFO 10:54:37,496 HelpFormatter - Executing as [email protected] on Linux 2.6.18-404.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13.
INFO 10:54:37,497 HelpFormatter - Date/Time: 2017/05/23 10:54:37
INFO 10:54:37,498 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:54:37,498 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:54:37,517 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:54:37,793 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 12:55:58,987 RMDTrackBuilder - Writing Tribble index to disk for file /data4/una/unag/GTEx.vcf.idx
INFO 12:56:03,976 GenomeAnalysisEngine - Preparing for traversal
INFO 12:56:03,987 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:56:03,989 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 12:56:03,989 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -1
at htsjdk.variant.variantcontext.GenotypeLikelihoods.getGQLog10FromLikelihoods(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute (
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.engine.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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
ERROR -------------------------------------------------------------------- ----------------------

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