Meganized reads not tallying with fastq read counts

Hi Team,

I ran diamond to generate ‘daa’ file. Then meganised using daa-meganizer command.

The total no. of fastq reads in the sample is “959741”. However, after maganizing it shows only “181,548” as total reads. May I know what happened to the rest?

Total reads: 181,548
With hits: 181,548
Alignments: 3,533,269
Assig. Taxonomy: 181,306

Many thanks in advance.

Kind regards,

Reads that don’t receive any alignments aren’t passed through

Many thanks Daniel, very helpful.