How to meganize a 2.5 Gb file via command line?

Hello, I’m new to the area and I have 5 .daa files to meganize and be able to open them in megan6 UE, how could I do this via the command line, if anyone can help me, I’d be grateful.

Hi I am glad you asked that question. I also just downloaded megan6 for command line and would like to know the best way to do this as well.

Here is what the manual says:
manual.pdf (

5.3 DAA Files
MEGAN can parse files in DAA format [5]. Note, however, that DAA files usually do not contain the names
of the taxa associated with the reference sequences and so one must supply suitable mapping files that map
identifiers used for the reference sequences to NCBI taxa and functional classes, see below.
In addition, the daa-meganizer program can be used to addition classification data and all necessary indices
to a DAA files so that it can be opened directly in MEGAN. It can be found in the tools directory

The program daa-meganizer prepares a DIAMOND DAA file for use with MEGAN, a process that we call
meganizing. The program performs taxonomic and functional classification of all reads in the given file and
then appends this information to the end of the file.
The program make-acc2ncbi can be used to create a new accession to taxonomy mapping file UE
from files downloaded from
The program make-gi2ncbi can be used to create a new GI to taxonomy mapping file from a
file such as or ftp:
The program references-annotator can be used to add taxonomic and functional annotation information to a
file of references before reads are aligned to the references. The annotations can then be parsed directly my
MEGAN or any of the MEGAN tools without the need to use mapping files.
See Section 20 for additional tools.


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Hi @kcristine were you able to figure this out? did anyone email you?


You need to download Megan tools: “To install MEGAN using a command-line dialog, launch the installer from the command line and pass the
command-line option -c. For example, under MacOS X, type the following:
-c” (

After that you can use the daa-meganizer tool, and you will also need a megan map which you can get from here: MEGAN6-download


There is a tutorial on how to perform meganization:

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