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Got error of java.lang.IllegalArgumentException: Invalid interval. Contig:81 start:0 end:69 with Fil

I have run 96 samples with somatic short variant calling pipeline with GATK version (gatk-4.1.4.0) and only three of them have this problem :java.lang.IllegalArgumentException: Invalid interval. Contig:81 start:0 end:69 when I run the code below:
gatk --java-options "-Xmx500m" FilterAlignmentArtifacts \
-R human_g1k_v37_decoy.fasta \
-V sample.filtered.vcf \ #come form Mutect2 After FilterMutectCalls
-I sample.sorted.out.bam \ #come from Mutect2
--bwa-mem-index-image hg37_reference.fasta.img \
-O sample.filtered.rm_artifacts.vcf.gz
So I really want to know how to fix this problem, I'v search this problem in forum but failed to find related themes.Please Help Me with best appreciation for GATK team

Answers

  • The whole error information is:
    java.lang.IllegalArgumentException: Invalid interval. Contig:81 start:0 end:69
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:731)
    at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:59)
    at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:35)
    at org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine.convertToInterval(RealignmentEngine.java:136)
    at org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine$$Lambda$291/1283441589.apply(Unknown Source)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502)
    at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
    at org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine.findJointAlignments(RealignmentEngine.java:107)
    at org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts.apply(FilterAlignmentArtifacts.java:234)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:131)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:106)
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:120)
    at org.broadinstitute.hellbender.engine.MultiVariantWalker$$Lambda$116/1442089085.accept(Unknown Source)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.Iterator.forEachRemaining(Iterator.java:116)
    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:163)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
    at org.broadinstitute.hellbender.Main.main(Main.java:292)
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @bioinfolearner

    There are two issues to note here:

    1) there is a Contig:81 start:0 end:69 in either the ref fasta, bam or img. Can you confirm where this is coming from? GATK tools use 1-based coordinate systems, however the error shows that there is a contig starting at 0.

    2) --bwa-mem-index-image argument should always be hg38. 'The reference passed with the -R argument must be the reference to which the input bam was realigned. This does not need to correspond to the reference of the BWA-MEM index image. The latter should be derived from the best available reference, for example hg38 in humans as of February 2018.' As mentioned in the doc here: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.4.0/org_broadinstitute_hellbender_tools_walkers_realignmentfilter_FilterAlignmentArtifacts.php

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