Illumina problems

I’m using dist.seq with 178K seqs and when I tried to use 20 processors it created a gigantic file; it left it running for >36h when I decided to stop it as the file was going to eat my drive. I just tried to use 1 processor and I see that the file is much smaller, albeit it is taking forever. I know that there are a few options as (slip option or setting up a different cutoff). Should I consider using these options with bigger projects and how would they impact data interpretation. Do you guys think I’m doing something wrong.

Any thoughts would be appreciated.

Can you give us some more details about what you’re doing from the beginning? Are you following the MiSeq SOP exactly?