Error using CombineGVCFs - Exception thrown at Chr
/Programs/gatk-4.2.5.0/gatk CombineGVCFs -R Genome.fasta -V mygvcfs.list -L Regions2423d.list -O 00.cohort.g.vcf.gz
org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at Chr09:702408 [VC /Volumes/Backup Plus/Database_Built_03:01:2022/GVCF2/1488.g.vcf @ Chr09:702408-1261180 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=1261180} GT=GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 filters=
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
at java.base/java.util.Iterator.forEachRemaining(Unknown Source)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:165)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.lang.ArrayIndexOutOfBoundsException
at java.base/java.lang.System.arraycopy(Native Method)
at java.base/java.util.Arrays.copyOfRange(Unknown Source)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.createIntermediateVariants(CombineGVCFs.java:228)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.apply(CombineGVCFs.java:174)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:133)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:108)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139)
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Hi Jugpreet Singh,
Thanks for writing in. How did you create these GVCFs? Could you try running ValidateVariants on your input files to try to input any potential issues? One thing to note is that CombineGVCFs will not work if your input file contains MNPs which would result in this type of error. Is it possible that your input GVCFs contain MNPs?
Kind regards,
Pamela
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Hi Pamela,
Thank you for getting back to me qucikly. I tried GenomicsDBImport, which works fine after removing some samples (probably causing the error for CombineGVCFs too).
Best regards,
Jugpreet
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Hi Jugpreet,
Thank you for trying that and letting me know. Are you now able to run CombineGVCFs successfully after removing those samples?
Kind regards,
Pamela
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Hi Pamela,
Thanks. I have not tried CombineGVCFs after that, but I can give it a try and let you know.
Bests,
Jugpreet
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Okay, sounds good!
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Hi Jugpreet Singh,
I just wanted to check in. Have you been able to run CombineGVCFs successfully?
Kind regards,
Pamela
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