Hi,
I have generated 26 GVCFs (with ploidy parameter=6), then run GATK-GenotypeGVCFs, successfully obtaining my genotype calls. Now I am trying to left normalize indels, using GATK-LeftAlignAndTrimVariants, and I get an ERROR MESSAGE.
The command line:
java -jar /home/tools/manual/GATK-3.7.0/GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R hg38/Homo_sapiens_assembly38.fasta --variant samples_6N.vcf -o samples_6N_LeftNorm.vcf --splitMultiallelics
The ERROR message:
##### ERROR --
##### ERROR stack trace
java.lang.IllegalStateException: Must initialize the cache of allele anyploid indices for ploidy 6
at htsjdk.variant.variantcontext.GenotypeLikelihoods.getAlleles(GenotypeLikelihoods.java:532)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.getLikelihoodIndexes(GATKVariantContextUtils.java:681)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.determineLikelihoodIndexesToUse(GATKVariantContextUtils.java:639)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.subsetAlleles(GATKVariantContextUtils.java:610)
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.splitVariantContextToBiallelics(GATKVariantContextUtils.java:1071)
at org.broadinstitute.gatk.tools.walkers.variantutils.LeftAlignAndTrimVariants.map(LeftAlignAndTrimVariants.java:212)
at org.broadinstitute.gatk.tools.walkers.variantutils.LeftAlignAndTrimVariants.map(LeftAlignAndTrimVariants.java:137)
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: Must initialize the cache of allele anyploid indices for ploidy 6
##### ERROR ------------------------------------------------------------------------------------------
Could you, please, help me with this problem? I could not find a similar discussion.
Thanks a lot!