ArrayIndexOutOfBoundsException when running MALT v0.52


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

java.lang.ArrayIndexOutOfBoundsException: Index 55248 out of bounds for length 36399
        at megan/megan.genes.GeneItemAccessor.getIntervals(
        at megan/megan.genes.GeneItemAccessor.annotateRefString(
        at malt/malt.AlignmentEngine.runInnerLoop(
        at malt/malt.AlignmentEngine.runOuterLoop(
        at malt/malt.MaltRun.lambda$launchAlignmentThreads$0(
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(
        at java.base/java.util.concurrent.ThreadPoolExecutor$
        at java.base/

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?


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.


I have uploaded a new release that should fix that problem