Description
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)