MEGAN6 can not display KEGG maps

yali · November 19, 2015, 10:18am

Dear Sir or Madam,

We met problem in MEGAN6 regarding KEGG maps.

The system background:
The computer system: OS X Version 10.9.3.
MEGAN version: 6.1.32beta
KEGG: latest version (map*.conf and map*.png files uploaded to class/resource/kegg)

What I did:
Import *.rma6 files. Then click the kegg viewer. However, no KEGG maps can show in MEGAN.

Here is a screenshot:
Then

Hope to get your help soon.

Thanks and regards,
Yang

Daniel · November 19, 2015, 2:27pm

Dear Yang,

due to licensing restrictions on KEGG, MEGAN does not ship with KEGG pathways. (MEGAN5 contained pathways dating back to 2011, before KEGG licensing changed.)
However, if you have a KEGG ftp license, then the Ultimate Edition of MEGAN allows you to view KEGG pathways within MEGAN using files downloaded from KEGG. To achieve this, using your licensed access to the KEGG ftp site, In this case, using your licensed access to the KEGG ftp site, download the KEGG files to a local directory.

Assuming that MEGAN 6 Ultimate Edition is installed in ~/megan and you have downloaded KEGG to ~/kegg, to enable visualization of KEGG pathways in MEGAN6, do the following:

mkdir ~/megan/class/resources/kegg
cd ~/megan/class/resources/kegg
tar xzf ~/kegg/xml/kgml/metabolic/ko.tar.gz
tar xzf ~/kegg/xml/kgml/non-metabolic/ko.tar.gz
mv ko/* .
mv map/.png .
cp ~/kegg/xml/kgml+/.xml .
tar xzf ~/kegg/pathway/map.tar.gz

This will give MEGAN access to all required files.

Then restart MEGAN6 Ultimate Edition. If you did everything correctly, then MEGAN will report KEGG bundled detected - will be able to display KEGG pathways in the message window, and you will be able to view KEGG pathways in the KEGG Viewer.

I am currently updating the user manual to explain exactly how to fully update MEGAN’s representation of KEGG if you have a KEGG ftp license.

yali · November 20, 2015, 9:59am

Thanks a lot Daniel. It works!

Flo · October 10, 2016, 2:42pm

Hello,

I was wondering if it is possible to update KEGG on the Community Edition as well, because we have a license for KEGG.

Thanks

Flo

Daniel · October 12, 2016, 6:47pm

At present, only the Ultimate Edition supports KEGG. In fact, KEGG is bundled into the UE.

Astrid · June 25, 2020, 8:16am

Hi Daniel,
I have a MEGAN6 UE trial version. How do I make it show KEGG pathways? The option “Show KEGG pathways…” is not lit up. I am running the program on Mac OS Mojave.
Please help!
Astrid

Daniel · June 30, 2020, 2:25pm

Did you meganize your DAA files or import your Blast files using the UE mapping database? megan-map-May2020-ue.db.zip
This contains the mapping to KEGG.
The KEGG analyzer is only available for files that have been meganized or created using that file.

Astrid · June 30, 2020, 3:44pm

Yes, my colleague imported the blast files using the UE mapping database on their Linux system and created .rma6 files. On their system he can view the KEGG pathways. When I open a file on my system, I get the following messages:

License valid until: 2020-07-12
Opening startup files
Loading ncbi.map: 2,249,459
Loading ncbi.tre: 2,249,463
Executing: open file=’/Users/Astrid/Desktop/Coldcrab/Astrid_MEGANfiles/trinity_king16_MC.Trinity.fasta_diamond_blastx_nr_eval.1e-9.rma6’;
Info: Opened file ‘trinity_king16_MC.Trinity.fasta_diamond_blastx_nr_eval.1e-9.rma6’ with 14,779 reads
Executing: openUE viewer=KEGG;
Loading kegg.map: 23,979
Loading kegg.tre: 53,636
Executing: zoom what=fit;

And here is a screenshot:

Daniel · July 6, 2020, 1:10pm

You have to uncollapse the hierarchy displayed on the right until you can see some of the pathway nodes on the right. Then you must select the one of interest on the right and then the Show KEGG Pathway context menu item will be enabled.
(Sorry, uncollapsing only on the left does not enable the menu item…)