Losing almost all reads after running deblur on paired-end sequences

[wasade (Daniel McDonald)]

@Mehrbod_Estaki

The reference hit is based on a positive filter using the 85% greengenes database so again if your sequences had non-biological sequences in them they might fail to hit the reference.

Just to clarify, the filter uses a 60% sequence identity against the 85% Greengenes OTUs. It is extremely permissive, but sufficient for filtering out things which are very unlikely to be 16S at all