Assembly problem in 2.11.0: java.lang.ArrayIndexOutOfBoundsException: Index 3 out of bounds for length 3

[cbrueffer]

Hi,

with GRIDSS 2.11.0 I see a an assembly exception across all input files I've tested; 2.10.2 works fine. The BAMs have all been aligned with bwa-mem2 2.2.1 and duplicates marked with biobambam2.

Commandline:

gridss \
        --threads 1 \
        --reference /scratch/references/hg38-noalt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
        --output TEST.vcf.gz \
        --assembly TEST_assembly.bam \
        --workingdir tmp \
        TEST.bam

INFO    2021-03-23 21:42:02     PositionalAssembler     Error during assembly of chromosome chr1 (13 reads in graph). Attempting recovery by rebuilding assembly graph.
java.lang.ArrayIndexOutOfBoundsException: Index 3 out of bounds for length 3
        at au.edu.wehi.idsv.debruijn.PackedSequence.getWordBases(PackedSequence.java:123)
        at au.edu.wehi.idsv.debruijn.PackedSequence.getKmer(PackedSequence.java:151)
        at au.edu.wehi.idsv.debruijn.ReadErrorCorrector.musket_two_sided(ReadErrorCorrector.java:95)
        at au.edu.wehi.idsv.debruijn.ReadErrorCorrector.errorCorrect(ReadErrorCorrector.java:70)
        at au.edu.wehi.idsv.debruijn.ReadErrorCorrector.lambda$errorCorrect$2(ReadErrorCorrector.java:50)
        at java.base/java.util.HashMap$KeySpliterator.forEachRemaining(HashMap.java:1603)
        at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:658)
        at au.edu.wehi.idsv.debruijn.ReadErrorCorrector.errorCorrect(ReadErrorCorrector.java:50)
        at au.edu.wehi.idsv.DirectedEvidenceErrorCorrectingIterator.ensureLastBucket(DirectedEvidenceErrorCorrectingIterator.java:54)
        at au.edu.wehi.idsv.DirectedEvidenceErrorCorrectingIterator.hasNext(DirectedEvidenceErrorCorrectingIterator.java:43)
        at com.google.common.collect.Iterators$5.computeNext(Iterators.java:635)
        at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:141)
        at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:136)
        at com.google.common.collect.Iterators$PeekingImpl.hasNext(Iterators.java:1127)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler$ReferenceIndexIterator.hasNext(PositionalAssembler.java:358)
        at com.google.common.collect.Iterators$PeekingImpl.hasNext(Iterators.java:1127)
        at au.edu.wehi.idsv.debruijn.positional.SupportNodeIterator.advance(SupportNodeIterator.java:219)
        at au.edu.wehi.idsv.debruijn.positional.SupportNodeIterator.ensureBuffer(SupportNodeIterator.java:211)
        at au.edu.wehi.idsv.debruijn.positional.SupportNodeIterator.hasNext(SupportNodeIterator.java:192)
        at com.google.common.collect.Iterators$PeekingImpl.hasNext(Iterators.java:1127)
        at au.edu.wehi.idsv.debruijn.positional.AggregateNodeIterator.process(AggregateNodeIterator.java:72)
        at au.edu.wehi.idsv.debruijn.positional.AggregateNodeIterator.ensureBuffer(AggregateNodeIterator.java:56)
        at au.edu.wehi.idsv.debruijn.positional.AggregateNodeIterator.hasNext(AggregateNodeIterator.java:37)
        at com.google.common.collect.Iterators$PeekingImpl.hasNext(Iterators.java:1127)
        at au.edu.wehi.idsv.debruijn.positional.PathNodeIterator.advance(PathNodeIterator.java:62)
        at au.edu.wehi.idsv.debruijn.positional.PathNodeIterator.next(PathNodeIterator.java:107)
        at au.edu.wehi.idsv.debruijn.positional.PathNodeIterator.next(PathNodeIterator.java:20)
        at com.google.common.collect.Iterators$PeekingImpl.peek(Iterators.java:1150)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.nextPosition(NonReferenceContigAssembler.java:356)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.advanceUnderlying(NonReferenceContigAssembler.java:417)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.advanceUnderlying(NonReferenceContigAssembler.java:368)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.ensureCalledContig(NonReferenceContigAssembler.java:270)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.hasNext(NonReferenceContigAssembler.java:194)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.flushIfRequired(PositionalAssembler.java:79)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:287)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:106)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.hasNext(PositionalAssembler.java:64)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:240)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:197)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.lambda$assembleBreakends$2(AssemblyEvidenceSource.java:100)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:834)

Log file and minimal example are attached.

gridss.full.20210323_210331.mito.saga.245892.log
gridss_minimal_reproduction_data_for_error_1.zip