I'm not familiar with MEGAN.
My issue is that when I import a blastx file (that appears to work) alongside a file with contigs in .fasta format (that it calls reads), it tells me that there are "no reads found". Any tips? I know it's difficult to address these issues with GUI programs as I don't have an command line output/input to show.
Thanks for any help you can suggest,
version: Creator: MEGAN (version 5.11.3, built 21 Jan 2016)