Malt-build ArrayIndexOutOfBoundsException

MALT: Megan Alignment Tool
1

Dear MEGAN community,

I have an error at malt-build step and currently I have no clue what can be the problem and I would really appreciate your help.

The script that I use is this:

malt-build -i /MALT/FASTA/*fna.gz -d /MALT/FASTA/OUT --sequenceType DNA --threads 10 --mapDB /NCBI_TAXONOMY_MALT/megan-nucl-Jan201.db --verbose

And this is the log file:

MaltBuild - Builds an index for MALT (MEGAN alignment tool)

Options:
Input:
–input: /MALT/FASTA/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz /MALT/FASTA/GCF_000001405.39_GRCh38.p13_genomic.fna.gz … (There are 722 *fna.gz files as total)…
–sequenceType: DNA

Output:
–index: index

Performance:
–threads: 10
–step: 1

Seed:
–shapes: default
–maxHitsPerSeed: 1000

Classification support:

Deprecated classification support:
–parseTaxonNames: true
–mapDB: /NCBI_TAXONOMY_MALT/megan-nucl-Jan201.db
–noFun: false

Other:
–firstWordIsAccession: true
–accessionTags: gb| ref|
–firstWordOnly: false
–random: 666
–hashScaleFactor: 0.9
–buildTableInMemory: true
–extraStrict: false
–verbose: true

Version MALT (version 0.5.3, built 4 Aug 2021)
Author(s) Daniel H. Huson
Copyright (C) 2021 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.

Classifications to use: Taxonomy
Reference sequence type set to: DNA
Seed shape(s): 111110111011110110111111
Deleting index files: 3
Number input files: 722

Loading FastA files:
100% (0.1s)

Caught:
java.lang.ArrayIndexOutOfBoundsException: Index -70 out of bounds for length 127
at malt/malt.data.DNA5.getNormalized(DNA5.java:64)
at malt/malt.io.FastAFileIteratorBytes.next(FastAFileIteratorBytes.java:159)
at malt/malt.data.ReferencesDBBuilder.loadFastAFile(ReferencesDBBuilder.java:179)
at malt/malt.data.ReferencesDBBuilder.loadFastAFiles(ReferencesDBBuilder.java:162)
at malt/malt.MaltBuild.run(MaltBuild.java:269)
at malt/malt.MaltBuild.main(MaltBuild.java:70)
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.MaltBuild.main(Unknown Source)

It breaks at the step of loading the files, so I have an assumption, that there can be some broken FASTA files in my folder, but unfortunately I cannot get it from the error.

The memory parameter is 1000GB. The size of all FASTA files is 32 GB.

Best,
Vasilina

2

Sorry for disturbing, the problem really was with FASTA files.

3

Could you post what is wrong with the FASTA files? I am also having the same index error for the NCBI nt database. I downloaded all the nt.*.tar.gz files, and when I run malt-build, i get ArrayIndexOutOfBoundsException error. Thnaks. Balaji.

4

Hi Balaji,

It appeared that when we downloaded multiple files with wget, it did not work well for a lot of files, the downloading was not finished and the compression was wrong. You can check all the files in your folder with this command, for example: gunzip -t filename, which reports if a file is not compressed correctly. We redownloaded the broken files after checking.
Hope it will work for you.

Best,
Vasilina