ArrayIndexOutOfBoundsException when running MALT v0.52

Bug Reports
1

Hello,

After having finally successfully build a MALT database using the latest version available from the website (v0.5.2), I always get the same Java ArrayIndexOutOfBoundsException error when aligning sequencing data to it:

malt-run \
    -J-Xmx200G \
    -d maltdb \
     -o malt_results \
     --mode BlastN \
     --alignmentType SemiGlobal \
    --inFile *.fastq.gz \
    --numThreads 40 \
    --replicateQueryCache \
    --minPercentIdentity 85.0 \
    --maxAlignmentsPerQuery 10 \
    --topPercent 1 \
    --minSupport 1 \
    --gapOpen 7 \
    --gapExtend 3 \
    --band 4 \
    --minPercentIdentityLCA 90.0 -v

resulted in

Caught:
java.lang.ArrayIndexOutOfBoundsException: Index 55248 out of bounds for length 36399
        at megan/megan.genes.GeneItemAccessor.getIntervals(GeneItemAccessor.java:105)
        at megan/megan.genes.GeneItemAccessor.annotateRefString(GeneItemAccessor.java:148)
        at malt/malt.AlignmentEngine.runInnerLoop(AlignmentEngine.java:358)
        at malt/malt.AlignmentEngine.runOuterLoop(AlignmentEngine.java:192)
        at malt/malt.MaltRun.lambda$launchAlignmentThreads$0(MaltRun.java:425)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
        at java.base/java.lang.Thread.run(Thread.java:832)

I tried older versions of MALT (v0.5, v0.5.1) but the error persists.

Does anyone have any suggestion what might cause this error message?

Cheers!

2

Hi, I’m having the same issue, and wanted to know if there’s a solution yet?

Oddly, I found that it runs successfully if I use malt v0.4.0, however the rma6 files have no taxonomy or functional annotations when I open them in MEGAN.

Thanks

3

I have uploaded a new release that should fix that problem