I am currently using MEGAN for my soil metagenomics. After using the latest version DIAMOND to get the DAA files, I imported these files to MEGAN along with GI mapping files (GI-Taxo, GI-KEGG, GI-SEED) downloaded from MEGAN6 website. The results show none of my sequences can be assigned to any function or taxonomy. Otherwise, the software said that my DAA files from DIAMOND are not DAA files.
Did anyone suffer this kind of situation before?
You need to use accession mappings, not GI mappings. If MEGAN says the DAA files are not DAA files, then you might have forgotten to set the file format in DIAMOND (DAA is not the default format).
You’re right, I should use Accession mappings instead of GI mappings.
Thank you so much.