Hello, can you please help me sort out the following error in running VariantsToBinaryPed:
java -jar /sb/project/fkr-592-aa/data/GalWaRat/bin/third/gatk-3.7/GenomeAnalysisTK.jar -T VariantsToBinaryPed -R /sb/project/fkr-592-aa/genomes/CfloGapsClosed6/Cflo_3.3_gaps_closed6.fasta -V /sb/project/fkr-592-aa/Danzqianqi/Cflo/WGS/filteredSNPss.vcf -m sample_phenotypeinfo2.fam --minGenotypeQuality 0 --bed filteredSNPss.bed --bim filteredSNPss.bim --fam filteredSNPss.fam
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/gs/scratch/zqianqi
INFO 19:31:00,898 HelpFormatter - ----------------------------------------------------------------------------------
INFO 19:31:00,901 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 19:31:00,902 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 19:31:00,902 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 19:31:00,902 HelpFormatter - [Tue Sep 05 19:31:00 EDT 2017] Executing on Linux 2.6.32-642.13.1.el6.x86_64 amd64
INFO 19:31:00,902 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_73-b02
INFO 19:31:00,906 HelpFormatter - Program Args: -T VariantsToBinaryPed -R /sb/project/fkr-592-aa/genomes/CfloGapsClosed6/Cflo_3.3_gaps_closed6.fasta -V /sb/project/fkr-592-aa/Danzqianqi/Cflo/WGS/filteredSNPss.vcf -m sample_phenotypeinfo2.fam --minGenotypeQuality 0 --bed filteredSNPss.bed --bim filteredSNPss.bim --fam filteredSNPss.fam
INFO 19:31:00,910 HelpFormatter - Executing as zqianqi@lg-1r17-n03 on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_73-b02.
INFO 19:31:00,911 HelpFormatter - Date/Time: 2017/09/05 19:31:00
INFO 19:31:00,911 HelpFormatter - ----------------------------------------------------------------------------------
INFO 19:31:00,911 HelpFormatter - ----------------------------------------------------------------------------------
INFO 19:31:00,922 GenomeAnalysisEngine - Strictness is SILENT
INFO 19:31:47,656 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 19:32:39,018 GenomeAnalysisEngine - Preparing for traversal
INFO 19:32:39,044 GenomeAnalysisEngine - Done preparing for traversal
INFO 19:32:39,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 19:32:39,045 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 19:32:39,046 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
ERROR --
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -1
at htsjdk.variant.variantcontext.GenotypeLikelihoods.getGQLog10FromLikelihoods(GenotypeLikelihoods.java:220)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.checkGQIsGood(VariantsToBinaryPed.java:442)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getStandardEncoding(VariantsToBinaryPed.java:406)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getEncoding(VariantsToBinaryPed.java:398)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.writeIndividualMajor(VariantsToBinaryPed.java:282)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:267)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:103)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: -1
ERROR ------------------------------------------------------------------------------------------
My .vcf file was made with HaplotypeCaller/GenotypeGVCFs/SelectVariants/VariantFiltration. I used ValidateVariants as well.
This is a snapshot of the .vcf file:
reference=file:///sb/project/fkr-592-aa/genomes/CfloGapsClosed6/Cflo_3.3_gaps_closed6.fasta
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 12 13 15 2 9
1 30 . T C 36.19 PASS AC=1;AF=0.100;AN=10;BaseQRankSum=0.712;ClippingRankSum=0.00;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=30.46;MQRankSum=1.98;QD=5.17;ReadPosRankSum=0.303;SOR=0.892 GT:AD:DP:GQ:PGT:PID:PL ./.:0,0:0:.:.:.:0,0,0 0/0:1,0:1:3:.:.:0,3,37 0/0:2,0:2:6:.:.:0,6,74 0/0:4,0:4:9:.:.:0,9,135 0/1:5,2:7:66:0|1:30_T_C:66,0,246 0/0:2,0:2:6:.:.:0,6,49
1 45 . A G 33.97 PASS AC=1;AF=0.100;AN=10;BaseQRankSum=1.09;ClippingRankSum=0.00;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.100;MQ=30.65;MQRankSum=2.20;QD=3.77;ReadPosRankSum=0.765;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL ./.:0,0:0:.:.:.:0,0,0 0/0:1,0:1:3:.:.:0,3,37 0/0:5,0:5:15:.:.:0,15,157 0/0:6,0:6:1:.:.:0,1,155 0/1:7,2:9:63:0|1:30_T_C:63,0,288 0/0:2,0:2:6:.:.:0,6,49
1 53 . C CA 24.57 PASS AC=1;AF=0.083;AN=12;BaseQRankSum=1.09;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.083;MQ=30.65;MQRankSum=2.20;QD=2.73;ReadPosRankSum=0.765;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL 0/0:1,0:1:3:.:.:0,3,37 0/0:1,0:1:3:.:.:0,3,37 0/0:5,0:5:15:.:.:0,15,157 0/0:6,0:6:1:.:.:0,1,169 0/1:7,2:9:63:0|1:30_T_C:63,0,288 0/0:2,0:2:6:.:.:0,6,49
My .fam file looks like this
Cflo 1 0 0 0 5047.16
Cflo 12 0 0 0 6249.9
Cflo 13 0 0 0 6007.21
Cflo 15 0 0 0 7123.6
Cflo 2 0 0 0 5581.36
Cflo 9 0 0 0 7462.87
Thank you! Please let me know if you require more information!