MG-RAST-Tools icon indicating copy to clipboard operation
MG-RAST-Tools copied to clipboard

Published 20 hours ago • verified publisher icon MG-RAST

Problem in installing and using `m5nr-tools.pl` & is there any other way to translate m5nr ids to KEGG (KO) ids?

Open jialiu232 opened this issue 3 years ago • 0 comments

Hello,

I want to download the KEGG annotated functional files for some MG-RAST soil samples. I used some code like this: curl "https://api.mg-rast.org/annotation/similarity/mgm4857466.3?identity=40&type=function&source=KO" > BG-Y2TE-B1ET9C12_blast.out and got some blast output files as shown in the image below. However, the second column is not KEGG Ortholog ID as I expected but m5nr id instead.

mg-rast-func-KO

I tried to install MG-RAST-Tools and plan to use m5nr-tools.pl to translate the m5nr ids into KEGG ID. But this was the error I got after the installation:

Screen Shot 2021-11-12 at 6 15 47 PM

To solve the problem, I added the mglib path to PERL5LIB, PERL50PT, and PYTHONPATH as shown in the pic below. I also checked the version of requests as shown below (I saw this suggestion in a past issue, not sure if it's necessary in my case).

Screen Shot 2021-11-12 at 6 16 35 PM

Screen Shot 2021-11-13 at 11 50 55 AM

But the same error still shows up. Could you give me any suggestions on this? Or is there any other tools that can convert the m5nr ids to KEGG KO ids?

jialiu232 avatar Nov 13 '21 17:11 jialiu232