Different numbers of assignments with each file of paired reads

I’m new to using megan and have some paired-read data I want to look at. I’ve aligned reads using diamond, and I’m importing the .daa files. If I use the R1 file, specify paired reads then the message window tells me it’s found 207 pairs, then gives me Reads=382,661, Assigned = 382,644. If I use the R2 file then it says 135 pairs, Reads = 359633, Assigned = 359611.

Have I misunderstood the paired reads function - surely it should give the same no matter which file you’ve told it to import?

For the paired read analysis to work, you need to import both files together.

(But rather than importing files, for performance purposes, you should have DIAMOND produce a DAA files and then meganize them. However, paired read mode doesn’t work for meganized DIAMOND files.)