Hi,
I tried to align sequences using malt-run
to a custom database of genomes downloaded from NCBI RefSeq. While the alignment it seems to be successful, I obtain the same error for each of my samples when analysing the alignments.
+++++ Aligning file: ../03-data/hg19_alignment.backup/CSM299_HG19unmapped.fastq.gz
Starting file: ../04-analysis/parasite/CSM299_HG19unmapped.rma6
10% 20% 100% (340.2s)
Finishing file: ../04-analysis/parasite/CSM299_HG19unmapped.rma6
Binning reads: Initializing...
Initializing binning...
Using Best-Hit algorithm for binning: Taxonomy
Binning reads...
Binning reads: Analyzing alignments
Caught:
java.lang.StringIndexOutOfBoundsException: begin 1000001, end 1000000, length 1000000
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:3756)
at java.base/java.lang.String.substring(String.java:1902)
at megan/megan.rma6.ReadBlockRMA6.read(ReadBlockRMA6.java:295)
at megan/megan.rma6.ReadBlockGetterRMA6.getReadBlock(ReadBlockGetterRMA6.java:99)
at megan/megan.rma6.AllReadsIteratorRMA6.next(AllReadsIteratorRMA6.java:77)
at megan/megan.rma6.AllReadsIteratorRMA6.next(AllReadsIteratorRMA6.java:32)
at megan/megan.algorithms.DataProcessor.apply(DataProcessor.java:213)
at megan/megan.core.Document.processReadHits(Document.java:547)
at malt/malt.io.RMA6Writer.close(RMA6Writer.java:245)
at malt/malt.MaltRun.launchAlignmentThreads(MaltRun.java:455)
at malt/malt.MaltRun.run(MaltRun.java:345)
at malt/malt.MaltRun.main(MaltRun.java:77)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at com.install4j.runtime/com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84)
at com.install4j.runtime/com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66)
at install4j.malt.MaltRun.main(Unknown Source)
Total reads: 16
With hits: 16
Alignments: 75
Assig. Taxonomy: 4
Binning reads: Writing classification tables
Numb. Tax. classes: 3
Binning reads: Syncing
Class. Taxonomy: 3
Analysis written to file: ../04-analysis/parasite/CSM299_HG19unmapped.rma6
Num. of queries: 18095318
Aligned queries: 152927
Num. alignments: 663294
The version of MALT was:
Version MALT (version 0.5.2, built 28 Jan 2021)
Author(s) Daniel H. Huson
and the command
malt-run -J-Djavax.accessibility.assistive_technologies=" " -J-XX:ParallelGCThreads=1 -J-Xmx400G -d ../03-data/refdbs/parasites_210705 -o ../04-analysis/parasite/ --mode BlastN --alignmentType SemiGlobal --inFile ../03-data/hg19_alignment.backup/*__HG19unmapped.fastq.gz --numThreads 48 --replicateQueryCache --minPercentIdentity 85.0 --maxAlignmentsPerQuery 10 --topPercent 1 --minSupport 1 --gapOpen 7 --gapExtend 3 --band 4 --minPercentIdentityLCA 90.0 -v
Does anyone have any suggestion what could have caused this issue?