I’m trying out new pipeline without aligning sequences (to see whether it improves otu clustering or not) and for removing PCR errors it suggests pre.cluster or shhh.seqs. Pre.cluster gives me an error because sequences are not aligned and so I’m running shhh.seqs. I have 137 000 unique sequences (16S V6 region) and so far shhh.seqs is still running after 9 hours (8 cpu, 32gb ram). Is it possible that this command is faulty? Or do I just have to wait and see?


Probably wait and see… Did you give it a group file?

Yes I included a group file. And after 12 hours server terminated this process. For now I just skip this step.