I am a student in master Bio and I have a project carried out on an archaeal community with 454.
My problems came from steps on chimeras.

mothur > chimera.uchime(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.names, group=GQY1XT001.shhh.good.groups, processors=2)
result : 00 :01 100.0% 0/73 chimeras found.

I do not know if my results are corect
I use that commonde after:

mothur > remove.lineage(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.pick.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.pick.names, group=GQY1XT001.shhh.good.pick.groups,, taxon=bacterria-unknown)

And later nothing more going, I have not found any contaminants.
My Proffesor asked us to achieve control without the use of a MOCK file (that we do not have), except that no MOCK I do not advance, I’m completely block.
If MOCK file is needed how to create it?

I really want to complete this project and see highlight the results obtained.

Can you help me please ???

If you didn’t sequence a mock community with your samples, then you need to skip those steps. In the future, I’d strongly encourage you to sequence a mock community in parallel with your samples.