RDP Assignment Detail import error


#1

Dear Megan Community,

I used Megan 6 community edition on windows to import RDP assignment detail result.

In general it worked well. There is a small problem I encountered regarding the naming of a few taxonomic level.

For example this particular read, the RDP assignment detail result is as follow:
M00319:12:000000000 BLPN7:1:1101:10001:11386;+;Bacteria;100%;“Actinobacteria”;100%;Actinobacteria;100%;Actinomycetales;100%;Corynebacteriaceae;100%;Corynebacterium;100%

However, when I import the file as rma6 file somehow the naming stopped at Class level and not followed by the family and genus names. Making the Genus not detected in the final result. Please see the attached image.

A few notes:
I tried MEGAN 5 with the same file, I did not have such problem
I tried importing other blastn result file (not RDP assignment detail) with MEGAN6 I also saw no problem on this.
This is only the case for a few classes, not all of bacteria classes. Most classes go all the way to Genus

I look forward to your response

regards,
Irvan


#2

This is because there is a difference between the RDP tree and the NCBI taxonomy used by MEGAN.

In the NCBI taxonomy, there are these two paths:

root; cellular organisms; Bacteria; Terrabacteria group; Actinobacteria ; Actinobacteria; Actinomycetales;
root; cellular organisms; Bacteria; Terrabacteria group; Actinobacteria ; Actinobacteria; Corynebacteriales; Corynebacteriaceae; Corynebacterium;

In MEGAN6, we use a conservative algorithm that matches the RDP classification path into the NCBI taxonomy, allowing omissions in either path (RDP or NCBI), but stopping when there is a major contradiction, as in the case for your data.


#3

Thank you for your reply

Is there a way around this? Such as downloading the latest NCBI map file?

regards,
irvan


#4

That will not fix the problem because RDP and NCBI simply disagree on the taxonomy, it is not a question of updating.

Workaround: remove all occurrences of Actinomycetales; from your RDP file, then this particular conflict between RDP and NCBI will be resolved.