Different results with -t rel_ab_w_read_stats and reads_map parameter

[fbeghini]

@xyxuq

But in the reads_map results (test.read_map.txt), there were quite a lot reads taxonomically assigned, not just species A in the rel_ab_w_read_stats results

From the help message:
reads_map: mapping from reads to clades (only reads hitting a marker)
This reports all the clades having at least a read mapping to a marker.

@xyxuq

Why the other species assigned with reads (reads_map result) were not included in the rel_ab_w_read_stats results? Which parameter control the species show up in the rel_ab_w_read_stats results?

In order to have a species identifies, you need to have at least 1/3 of the markers covered by reads, then a robust average is calculated using a subset of them. You can increase the fraction of those markers by tweaking the stat_q parameter (see Relaxing classification parameters - #2 by fbeghini)