Hi @simon,
If you are indeed sequencing via a 2x150 kit with the EMP V4 (515f-806r primers), and those primers are actually contained within the reads… then sadly these reads will either be to short, or not have enough enough high-quality bases, for merging.
The 2x150 sequencing approach works best when using the sequencing strategy outlined here, and the references therein. That is, when using a 2x150 for the V4 region, the sequencing strategy used should NOT sequence through the primers. Meaning, there would not be any primers in the reads. So no need for cutadapt. This saves ~40 bp, which increases the ability to sequence further into the read, allowing for longer overlapping segments, for better merging of the reads. This saves costs too as you can get away with a 2x150 sequencing run.
Otherwise, if the primers are contained within your reads (which have to be trimmed via cutadapt), you’ll often have to use a 2x250 sequencing run to guarantee longer reads with enough overlap in order to merge.
At least these are common factors I’ve run into when using 2x150 vs 2x250 for sequencing the V4 region. Hopefully, others will have recommendations / comments. 