ecotoag assigns only very small proportion of reads
I finally managed to run ecotag but it only assigns a small proportion of my reads.
fabian$ obi stats -c SCIENTIFIC_NAME /Volumes/Elements/COI_dms/COI_99_assigned 2020-04-29 11:21:45,535 [stats : INFO ] obi stats 99.9 % |#################################################| ] remain : 00:00:0 SCIENTIFIC_NAME count total None 1736 1736 Mesangiospermae 3 3
2020-04-29 11:22:41,038 [count : INFO ] obi count /Volumes/Elements/COI_dms/COI_99_assigned 1846 1846
(the same is true for my 16S reads)
This is surprising as I used the full EMBL database and cast a rather wide net.
I ran obi build_ref_db with -t 0.97 and ecotag with -m 0.97 (following the tutorial). I am not sure what exactly this does and if it could be the culprit. The other option would be that something got wrong in ecopcr, maybe in the orientation of the primers?
best
Fabian