MALT Index issues

MALT: Megan Alignment Tool
1

Hi,
I´m using MALT for the first time and I have some doubts about building the index.
My command line for malt-build is :

malt-build -i /mnt/Archives/BLAST_databases/nt/. -d Index -a2taxonomy /mnt/Cromosoma/mbravo/malt/data/gi_taxid-March2015X.bin --sequenceType DNA

It creates the following files:
index0.idx ref.idx table0.db table0.idx

But those files were empty.

I then did the following:
malt-run -i /mnt/Cromosoma/mavila/vvilla/samples/Unmappedreads/ -d ./Index -m BlastN -o

It says:
Index is too old or incorrect file (wrong magic number). Please recompute index.

I don´t know what I`m doing wrong. I will appreciate any comment.

Thank you.

Miriam

2

Hi Miriam,

Do you have the log output of malt-build (standard-out)? I’d also recommend using the -v command (verbose) to give you more information.

My initial thought is that you need to specify the file properly, i.e. malt-build -i /mnt/Archives/BLAST_databases/nt/nt.gz

Cheers,
Raphael

3

Hi ElsenRa,

For malt-build this is the script that I using:

malt-build -i /mnt/Cromosoma/mavila/mbravo/nr_database/nr.gz -d Index -a2taxonomy /mnt/Cromosoma/mavila/mbravo/malt/data/nucl_acc2tax-Oct2017.abin.zip --sequenceType DNA --verbose

It says;

Options:
Input:
–input: /mnt/Cromosoma/mavila/mbravo/nr_database/nr.gz
–sequenceType: DNA
Output:
–index: Index
Performance:
–threads: 32
–step: 1
Seed:
–shapes: default
–maxHitsPerSeed: 1000
Classification:
–classify: Taxonomy
–acc2taxonomy: /mnt/Cromosoma/mavila/mbravo/malt/data/nucl_acc2tax-Oct2017.abin.zip
–parseTaxonNames: true
Other:
–firstWordIsAccession: true
–accessionTags: gb| ref|
–firstWordOnly: false
–random: 666
–hashScaleFactor: 0.9
–verbose: true

But the files that created were empty: index0.idx ref.idx table0.db table0.idx

It could be the file that I´m using acc2taxonomy?

Thank you so much for your answer!!!

Miriam

4

Hi Miriam,

The nr is a protein database, so you’ll need to set --sequenceType to Protein. Additionally, you’ll want to use the prot_acc2tax-Oct2017X1.abin.zip file as your –acc2taxonomy mapping file.

Let me know if this works, if not, could you please provide the full output (including errors)?

Cheers,
Raphael

5

Hi Raphael,

I made a mistake in the previous script, I used the BLAST nt batabase, so the script is

malt-build -i /mnt/Archives/BLAST_databases/nt/. -d Index -a2taxonomy /mnt/Cromosoma/mavila/mbravo/malt/data/nucl_acc2tax-Oct2017.abin.zip --sequenceType DNA

and the files from the Idex still empty.

I don`t know what else to do, :frowning:

Best, Miriam

6

Hi Miriam,

Can you provide the full log output using the -v command?

Cheers,
Raphael

7

Hi Raphael,

This is the full log output:
Output:
–index: Index
Performance:
–threads: 64
–step: 1
Seed:
–shapes: default
–maxHitsPerSeed: 1000
Classification:
–classify: Taxonomy
–acc2taxonomy: /mnt/Cromosoma/mavila/mbravo/malt/data/nucl_acc2tax-Oct2017.abin.zip
–parseTaxonNames: true
Other:
–firstWordIsAccession: true
–accessionTags: gb| ref|
–firstWordOnly: false
–random: 666
–hashScaleFactor: 0.9
–verbose: true
Version MALT (version 0.4.0, built 6 Sep 2017)
Copyright © 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Reference sequence type set to: DNA
Seed shape(s): 111110111011110110111111
Deleting index files: 3
Reading file: /mnt/Archives/BLAST_databases/nt/nt.00.nhd
10% 100% (0.6s)
Reading file: /mnt/Archives/BLAST_databases/nt/nt.00.nhi
100% (0.0s)
Caught:
java.lang.ArrayIndexOutOfBoundsException: -60
at malt.data.DNA5.getNormalized(DNA5.java:64)
at malt.io.FastAFileIteratorBytes.next(FastAFileIteratorBytes.java:159)
at malt.data.ReferencesDBBuilder.loadFastAFile(ReferencesDBBuilder.java:153)
at malt.data.ReferencesDBBuilder.loadFastAFiles(ReferencesDBBuilder.java:134)
at malt.MaltBuild.run(MaltBuild.java:200)
at malt.MaltBuild.main(MaltBuild.java:58)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:65)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

Thank you!!
Miriam

8

Hi Miriam,

/mnt/Archives/BLAST_databases/nt/nt.00.nhd

It looks like the file you’re trying to use is not right. How did you download the nt database? It should be gzipped (nt.gz), and be roughly 40GB. Try this link: ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz

Cheers,
Raphael