abra2 error java.lang.NumberFormatException

[C-YONG]

Hello, I have constructed a graph-based pan-genome using MC, and then I used VG to align short-read data to the pan-genome. When I used abra2, the following error occurred. What could be the reason for this?? Thank you in advance for your help, Yong

error： java -Xmx20G -Xmx20G -jar /home/chiyong/miniconda3/envs/gatk3.8/share/abra2-2.24-3/abra2.jar
--tmpdir /mnt/c/pan-genome/Minigraph-Cactus/TMP/
--targets /mnt/c/pan-genome/Minigraph-Cactus/pangenome/sampling/bam/CF108.left.shifted.intervals.widened.bed
--in /mnt/c/pan-genome/Minigraph-Cactus/pangenome/sampling/bam/CF108.lefted1.sorted.bam
--out /mnt/c/pan-genome/Minigraph-Cactus/pangenome/sampling/bam/CF108.indel.realigned.bam
--ref /mnt/c/pan-genome/data/T2T.fasta
--index
--log warn
--threads 85 INFO Wed Dec 04 22:56:12 CST 2024 Abra version: 2.24 INFO Wed Dec 04 22:56:12 CST 2024 Abra params: [/home/chiyong/miniconda3/envs/gatk3.8/share/abra2-2.24-3/abra2.jar --tmpdir /mnt/c/pan-genome/Minigraph-Cactus/TMP/ --targets /mnt/c/pan-genome/Minigraph-Cactus/pangenome/sampling/bam/CF108.left.shifted.intervals.widened.bed --in /mnt/c/pan-genome/Minigraph-Cactus/pangenome/sampling/bam/CF108.lefted1.sorted.bam --out /mnt/c/pan-genome/Minigraph-Cactus/pangenome/sampling/bam/CF108.indel.realigned.bam --ref /mnt/c/pan-genome/data/T2T.fasta --index --log warn --threads 85] java.lang.ArrayIndexOutOfBoundsException: Index 5973 out of bounds for length 5599 at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:311) at htsjdk.samtools.DiskBasedBAMFileIndex.getSpanOverlapping(DiskBasedBAMFileIndex.java:60) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:751) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:434) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:523) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:390) at abra.MultiSamReader.(MultiSamReader.java:40) at abra.ReAligner.processChromosomeChunk(ReAligner.java:262) at abra.ReAlignerRunnable.go(ReAlignerRunnable.java:21) at abra.AbraRunnable.run(AbraRunnable.java:20) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) java.lang.ArrayIndexOutOfBoundsException: Index 5515 out of bounds for length 5504 at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:311) at htsjdk.samtools.DiskBasedBAMFileIndex.getSpanOverlapping(DiskBasedBAMFileIndex.java:60) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:751) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:434) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:523) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:390) at abra.MultiSamReader.(MultiSamReader.java:40) at abra.ReAligner.processChromosomeChunk(ReAligner.java:262) at abra.ReAlignerRunnable.go(ReAlignerRunnable.java:21) at abra.AbraRunnable.run(AbraRunnable.java:20) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583)