Meganizer DAA file ArrayIndexOutOfBoundsException Error

Hi.

I have been following the protocol from Arumugam et al. 2019 for frame read correction and am having trouble meganizing my daa files. I am receiving an out of bounds error message and no taxonomy mapping. I’m just wondering if it is a bug or my error.

Thanks for any help you can give on this!

Diamond was run as follows, with a version of the nr database downloaded this week:

diamond blastx --range-culling --top 10 -F 15 --outfmt 100 -c1 -b12 -t /dev/shm -p 44 --query inputfile -d nr --out output_file

I have tried to meganize the resulting daa file using the command line and gui version of the meganizer, using the megan-map-Oct2019.db (unzipped) as the database.

I am hitting an “ArrayIndexOutOfBoundsException” error in with both extended and fast annotation modes.

Logs from GUI as follows:

Fast mode:

Meganizing file: input.daa
Annotating DAA file using FAST mode (accession database and first accession per line)
Initializing binning…
Using ‘Interval-Union-LCA’ algorithm (51.0 %) for binning: Taxonomy
Using Multi-Gene Best-Hit algorithm for binning: SEED
Using Multi-Gene Best-Hit algorithm for binning: EGGNOG
Using Multi-Gene Best-Hit algorithm for binning: INTERPRO2GO
Binning reads…
ArrayIndexOutOfBoundsException: Index 27 out of bounds for length 27
Total reads: 0
With hits: 0
Alignments: 0
Assig. Taxonomy: 0
Assig. SEED: 0
Assig. EGGNOG: 0
Assig. INTERPRO2GO: 0
Class. Taxonomy: 0
Class. SEED: 0
Class. EGGNOG: 0
Class. INTERPRO2GO: 0
Loading MEGAN File: input.daa

Extended mode:

Meganizing file: input.daa
Annotating DAA file using EXTENDED mode
Error: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 14
java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 14

Are you sure the DAA file is complete. Good way to check: does DIAMOND complain when you attempt to use the view command to extract alignments in a different format?

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