MetaPhlAn2: no taxonomy annotated for some samples

Hi, we have some shotgun sequencing data and for some of our samples, after running Metaphlan, no taxonomy is annotated for those samples. The sequencing quality seems fine, with even more reads than other samples successfully analyzed by Metaphlan (after human reads and contaminants removed). Any idea why this is happening?

Hi, which is the source of those metagenomes?

Hi, so the material sequenced were gastric fluids. They seem to have a lot of bacterial DNA (we analyzed 16S copy number previously by qPCR).

I’d try to use a lower stat_q value--stat_q 0.1 first in order to see if more makers are used for the species identifications, if not, MAPQ can be blamed, by default MetaPhlAn 3 filters out alignments with MAPQ values below 5, you can deactivate the filtering by using --min_mapq_val -1