Hi,
I converted 1000G_phase3_v4_20130502.sites.vcf to hg19 using Picard 2.10.0 with the following command:
java -Xincgc -Xmx5G -jar /data/home/hhx037/picard-tools/picard.jar LiftoverVcf I=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/b37/1000G_phase3_v4_20130502.sites.vcf O=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.sites.vcf CHAIN=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/liftover/b37tohg19.chain REJECT=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.liftover_rejected.vcf R=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta
and when running CalculateGenotypePosteriors I get the following error:
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
OpenJDK 64-Bit Server VM warning: If the number of processors is expected to increase from one, then you should configure the number of parallel GC threads appropriately using -XX:ParallelGCThreads=N
INFO 13:02:12,260 HelpFormatter - ----------------------------------------------------------------------------------
INFO 13:02:12,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 13:02:12,267 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 13:02:12,267 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 13:02:12,267 HelpFormatter - [Sat Jul 08 13:02:12 BST 2017] Executing on Linux 3.10.0-514.16.1.el7.x86_64 amd64
INFO 13:02:12,267 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_131-b12
INFO 13:02:12,270 HelpFormatter - Program Args: -T CalculateGenotypePosteriors -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -V /data/WHRI-Panos-Scratch/hhx037/piperi/filtered/piperi_snps_indels.vcf --supporting /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.sites.vcf -ped /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped -o ./refined/piperi_snps_indels.postCGP.vcf
INFO 13:02:12,274 HelpFormatter - Executing as hhx037@nxv27 on Linux 3.10.0-514.16.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b12.
INFO 13:02:12,275 HelpFormatter - Date/Time: 2017/07/08 13:02:12
INFO 13:02:12,275 HelpFormatter - ----------------------------------------------------------------------------------
INFO 13:02:12,275 HelpFormatter - ----------------------------------------------------------------------------------
INFO 13:02:12,496 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:02:12,813 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:02:13,584 PedReader - Reading PED file /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped with missing fields: []
INFO 13:02:13,599 PedReader - Phenotype is other? false
INFO 13:02:13,882 GenomeAnalysisEngine - Preparing for traversal
INFO 13:02:13,890 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:02:13,890 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:02:13,890 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:02:13,891 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtimeERROR --
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 2
at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.getLikelihoodsAsMapSafeNull(FamilyLikelihoodsUtils.java:455)
at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.updateFamilyGenotypes(FamilyLikelihoodsUtils.java:392)
at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.calculatePosteriorGLs(FamilyLikelihoodsUtils.java:263)
at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:345)
at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:189)
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
Is this caused by the liftover or it's a different issue? Any idea how to fix this?
Cheers,
Steph