Hi @moshhoss,
It looks like some samples do not have sequences long enough for the trim length specified. The primers have already been removed for these data so that is not be needed. I've never attempted merging R1/R2 for these data -- is it possible that one or a few of the samples had no successfully stitched reads?
For context, I'm the Scientific Director for the American Gut Project.
Please note too that if you'd like pre-computed Deblur feature tables, they can be obtained using redbiom against study 10317.
Best,
Daniel