I’ve tried the above guidelines and when I import my .rma files into MEGAN, none of the reads could be assigned to anything. There is basically always a long line between the root and the bubble that says “not assigned” with nothing inbetween. Do you have any suggestions what might be causing this? Am I perhaps using the wrong GI-to-NCBI mapping files? I’ve downloaded them from there: http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html .