I like to use MEGAN5 for analyzing bins sorted from asembled metagenomes.
I since I have Blast results (against nr) in tabular format, I usually just use the "Import from BLAST"-option from the "File" Menu and specify a GI-mapping file to get obtain the taxonomy info for the blast results. (Similar I would use SEED- and KEGG- mapping files to obtain functional info).
Since I have a large number of bins that i want to analyze, it is getting rather tedious to click through the menus by hand.
Therefore I want to use the command-line interface of MEGAN5 to automize those tasks.
loading the gi mapping file seems pretty straightforward:
Importing the Blast-File is also pretty straightforward:
import blastFile=blastp_nr.out.tab fastaFile=bin_79_allmarkers.faa meganFile=delmetest.rma
When I run the two above commands, first the mapping file is successfully imported, and then the BLAST-file is imported. However the taxon names are not being mapped, resulting in 100% unassigned reads.
Probably i have to use the "mapping=<mapperConfiguration>" argument when importing the blast file, but i have no idea what to give as actual argument. I can't find any info on how to set the "mapperConfiguration". I've tried simply passing "mapping=YES" as argument, but that didn't help.
Does anyone have experience on using MEGAN5 though the command-line interface?