Paired end vs. Read 1 analysis?

I’m trying to build a pipeline for functional analysis of soil shotgun metagenomics data (paired-end reads). Running daa2rma with the separate R1 and R2 daa files is taking a crazy long time, even with 64 cores, 512GB memory. Any thoughts on using just R1 reads for read-based functional/taxonomic analysis? I am also doing assembly-based analysis, but don’t want to lose all the information from lower abundance organisms…

I am sorry that daa2rma is so slow, whereas daa-meganizer can’t use the paired-end info… Unfortunately, I don’t have any good ideas here.