I also don't understand why some reads are not assigned. One example can be broken down to one hit like
query1 gi|998520486|ref|XP_015521226.1|tax|441921| 100.000 8 0 0 1 8 92 99 57 31.2
I expected that the read was assigned to Neodiprion lecontei, as the taxid is correctly interpreted my MEGAN. However, the read is not assigned. Min Score is set to 1, Max Expected to 1000, Min Support Percent to 0 (off), Min Support to 1. (Actually, the read has many more hits.) Am I missing something? Thanks for any suggestions.