Thanks for your information. Sorry that I don't much knowledge about swarm. According to wiki, you can run the pipeline as step1~ step4.
Because chimera and non-chimeras will cluster independent OTU, that means you can pick representative sequence (rep_set) after OTU clustering.
According to the result of pick_otus.py, use pick_rep_set.py to pick rep_set, use this rep_set (fasta file) as input file of vsearch to filter chimeras.
I have run swarm on my data with QIIME 1.91. successfully got rep_set of each OTU.
command is below,
pick_otus.py -i seqs.fna -o otus_swarm -m swarm
pick_rep_set.py -i ./otus_swarm/seqs_otus.txt -f seqs.fna -o rep_set.fna
But I don't have vsearch. so I cant't run the total pipeline.