Convert DAA file to RMA file

User Questions
1

Dear Dr.Daniel and everyone,

I use DIAMOND and MEGAN for the first time to analyze my sample from soil in HPCC server. I’ve got DAA file and I want to convert it into the RMA file.
I’ve download database from MEGAN download page

https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-map-Oct2019.db.zip

and

https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html

and then I convert the file following the generic pipeline for DIAMOND and MEGAN6, but it doesn’t work.
I also read this thread http://megan.informatik.uni-tuebingen.de/t/kegg-data-for-daa2rma-command/1366?u=lulunisrna

from that thread I get that I didn’t need to use parameters parameters such as --acc2taxa, --acc2eggnog and --acc2interpro2go but I can use --mapDB parameter.

But, when I run the command line with --map parameter it’s doesn’t work.
And then, I tried to run with this command line daa2rma -i alignment/HA_result.daa -o megan/HA_result.rma and it’s work.

I got the result like this:

Version   MEGAN Community Edition (version 6.12.3, built 14 Aug 2018)
Copyright (C) 2018 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Loading ncbi.map: 1,787,384
Loading ncbi.tre: 1,787,388
In DAA file:  alignment/HA_result.daa
Output file:  megan/HA_result.rma
Classifications: Taxonomy
Parsing file: alignment/HA_result.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1312.4s)
Total reads:         1,032,425
Alignments:          6,618,743
100% (0.0s)
Binning reads: Initializing...
Initializing binning...
Using 'Naive LCA' algorithm for binning: Taxonomy
Binning reads...
Binning reads: Analyzing alignments
Total reads:        1,032,425
With hits:           1,032,425
Alignments:          6,618,743
Assig. Taxonomy:             0
MinSupport set to: 516
Binning reads: Applying min-support & disabled filter to Taxonomy...
Min-supp. changes:           0
Binning reads: Writing classification tables
Numb. Tax. classes:          1
Binning reads: Syncing
Class. Taxonomy:             1
100% (1034.5s)
Total time:  2357s
Peak memory: 2.0 of 2.1G

I don’t know the result is true or false for the analysis because I also read threads from MEGAN and the output is not like my output that I get.

Pleas guide me and give me an advice.

Thank you for your help.

Regards,
Lulu

2

Dear Lulu,

please use daa-meganizer and not daa2rma.
daa-meganizer prepares a daa file for opening in MEGAN.
The program is much faster than daa2rma and has the advantage that a second file is not created.

Then make sure that you have the very latest release of MEGAN, as the --mapDB option is new.

Run the program with option -h (or no options) to get a full printout of available options. You should see this:

Classification support:
-mdb, --mapDB [string] MEGAN mapping db (file megan-map.db).

MEGAN uses the mapping file to assign aligned reference sequences to taxonomic and functional classes. Without it, none of your reads will be assigned.

3

Dear Daniel,

Thank you for your reply.
Actually I have meganize the .daa file using MEGAN GUI because I can not convert .daa to .rma using CLI. Am I can have the same result between meganize the .daa file using GUI and CLI? I used database from MEGAN download file.

4

You appear to be using a very old version of MEGAN (2018), please update to the most recent version, and then the command line tools will work.

5

Dear Daniel,

Thank you so much for your reply. How I can update MEGAN to the latest version? Sould I uninstall it and then download MEGAN from MEGAN download file again?

Thank you

6

Please use the Window -> Check For Updates menu item