Hello, I am using MEGAN6 with the latest mapping file (megan-nucl-Oct2019) to process my blastn results.
For some reason a great number of reads (more than 30,000), most of them with excellent hits against the same taxon, are being placed in the “Not assigned” node. To exemplify, these are the blastn results for one of those reads (the homology search was set to show the 5 best hits) indicating they all correspond to the same taxon (Spodoptera frugiperda) with an unequivocal E-value (0.0):
Query= HJK3X6U01BD2KC, 470 bp.
Sequences producing significant alignments: Score (Bits) E-Value
NJHR01000880.1 Spodoptera frugiperda isolate Sf9 scaffold880, who… 673 0.0
NJHR01000167.1 Spodoptera frugiperda isolate Sf9 scaffold167, who… 673 0.0
NJHR01001202.1 Spodoptera frugiperda isolate Sf9 scaffold1202, wh… 673 0.0
LS001813.1 Spodoptera frugiperda strain corn strain genome assemb… 667 0.0
LS041536.1 Spodoptera frugiperda strain corn strain genome assemb… 667 0.0
I checked the submission date for these particular accessions to make sure they weren´t from a later date than that of the mapping file: they are from June and December 2017 so that shouldn´t be a problem as the mapping file is from October 2019.
I´d be very grateful if you could help me out with this.