Re: Kegg and seed analysis


#1

Hi everyone!

I am using Megan 5 for Metagenomic analysis and I tried kegg and seed analysis using command line in Ubuntu 14.04. But I couldn’t get any output results for Kegg. I am using “BlastNT.xml” file as my blast input file and “gi_taxid-March2015X.bin”," gi2kegg-Feb2015X.bin", “gi2seed.map” as mapping files.

The phylogenetic tree was generated but the kegg and seed analysis couldn’t be performed.Previously, I also tried using GUI mode for the same analysis but it showed “not assigned” and “no hits”

The command used:

load taxGIFile=’/home/simang/mapping/gi_taxid-March2015X.bin’;
load keggGIFile=’/home/simang/mapping/gi2kegg-Feb2015X.bin’;
load seedGIFile=’/home/simang/mapping/gi2seed.map’;
import blastfile=’/home/simang/samples/sample_1/contigs_fa_blastNT.xml’ meganfile=’/home/simang/commandline_try11.rma’;
set useKegg=true;
set useSeed=true;
quit;

Below I am attaching my output. Anybody please help me out.
Thank you in advance!!