Problem to import RDP Classifier file


#1

Hi,

I’m trying to import the RDP Classifier (Standalone, version 2.12) output file to Megan 6.11.1, but it is not recognizing the format file.

I have tested the same input file on Megan 5.11.3 and it’s ok.

When I get the result using RDP Website (Assignment Detail), it only can identify the first taxon-name, ex: Bacteria, and ignores all the other results, even with high score (> 90%).

I’m using Linux Centos 6.9

Thanks.
Mauricio


#2

Please send me an example and I’ll take a look at it


#3

Hi Daniel,

I picked up 10 reads and ran the RPD Classifier v 2.12.

In the attached zip file you can find the 10 reads fasta file (“10_reads.fasta”), the rdp_classifier output (“10_reads_classifier_v2.12.txt”) and a file with the error when I try importing the rdp classified file (“Error_Megan_Imput_rdp_Classifier.png”).

I have run the same rdp_classifier output file (“10_reads_classifier_v2.12.txt”) in Megan v5.11.3 and it’s ok, as you can check it (“10_reads_classifier_v2.12_megan5.rma”).

File downloaded from RDP website works when I change the Megan parameter “Max number of matches per read” to larger than 1 (10 for instance), but in Megan5 I have used the value 1 and it always worked.

Thanks
Mauricio


#4

Dear Mauricio,

thanks for your bug report. There were multiple issues with the RDP analysis implementation in MEGAN6. Using the data you sent me, I was able to identify and fix them. Now MEGAN6 is able to correctly parse files produced by the standalone RDP classifier and also now ignores the “max number of matches per read” setting, as it should do.
I have uploaded a new release with these fixes (6.11.2)
D


#5

Hi Daniel,

Now it’s Ok.

Thanks
Mauricio


#6

Hi Daniel,

I have updated Megan to version 6.11.4 and the analysis of standalone rdp_classifier stopped working again.

When I back to previous version 6.11.2 it’s ok.

Thanks.
Mauricio


#7

sorry, this works again in release 6.11.5