sortmerna + sumaclust added to the open reference OTU picking pipeline

No, pre-filtering is not possible because it's done internally by SortMeRNA. The purpose of the pre-filter, if I understand correctly, is to remove non-rRNA sequences, which is what the E-value does as well. The read IDs that are output to the failures file are all reads that didn't align with threshold id & coverage, but do pass the E-value, so all of them are considered as rRNA and can be used for de novo clustering. 

The option --other (in sortmerna) would output all reads not passing the E-value threshold, and these equal to the reads filtered out by the pre-filter. However, I don't set this option and we don't need those reads.