On the page 44 of User Manual for MEGAN V6.4.12, you indicted there is a option to select input data as paired-read (see blow),
The Paired Reads item is used to turn paired-read awareness of MEGAN on and off. In paired read mode, MEGAN utilities read-pairing information to enhance the taxonomic assignment of reads.
But actually in the MEGAN V6.4.15, there is no such option (see screenshot).
Would you take a look? thanks,