Hello Daniel, thank you for your question.
To start, we are using DIAMOND ver 0.8.22 in conjunction with MEGAN ver 6.5.8. MEGAN is implemented on a cluster and has access to 64 Gb RAM. DIAMOND is outputting DAA files using the command
diamond blastx --db nr_22-08-2016_db --query input.fasta --min-score 55 --out output_OUT --threads 80 --block-size 7.0 --index-chunks 1 --outfmt 100 --tmpdir /das_data/
We have downloaded mapping files for Taxonomy, SEED, EggNOG and Interpro2GO from the DIAMOND6 download page and the KEGG mapping file from the MEGAN5 download page. (We have used MEGAN5 for a while and found it very useful).
I have currently been working on a collection of 7 metagenomes. In the MEGANIZER window I have used mapping files for all tabs (ie. taxonomy, eggNOG, Interpro2GO, SEED and KEGG) and weighted LCA at 80%. Consistently, the output DAA files are mapped successfully in all cases except for the taxonomy. I have tried using the nucl-acc2taxid-August2016 and the nucl-gi2taxid-August2016 both individually and together but without success. I have downloaded and unzipped the files for a second time just in case the first were corrupted but still with no success. I am sure that I am doing something wrong but cannot see where.
Any help you can provide Daniel would be much appreciated