pick_de_novo_otus.py -o denovo_splitfastq_uninhab_swarm -i seqs.fna -p param_files/swarm_params.txt
swarm_params.txt I wrote in textwrangler and contains only one line:
However, the output seems to be identical (identical number of OTU's picked) as the uclust method when I don't include a parameter file. Also, I notice that when it runs, at the top of terminal, it says swarm for only a second as it runs, and then uclust appears instead for most of the run time. Does anyone know what I am doing wrong here and how I can get swarm pick my OTU's?
Thanks very much!
I was expecting swarm to identify quite a lot fewer OTU's than uclust