I am removing chimeras and singletons via chimera.vsearch and split.abund in mothur. After split.abund, I used summary.seqs, but it gave me an error message:
[ERROR}: Your name file contains 175504 sequences, but your fasta file contains 173083. File mismatch detected, quitting command.
I tried this multiple times and also made sure the commands were completely finished. I also used only 1 processor.