how make groups from my library?

Dear all
1- I am facing problem and I need help. I have 2 library each one had 60 samples from different site. I upload the 2 fasta files and merge files. now I need to make group by samples since each samples from different sites
2- when I run chimera.vsearch command, the out put should be 3 not 2 I am missing chimera. vsearch count table, why? I run before on other date and was done
3- i get one line in graph when I run plotting tool?
4- beta diversity is done but file is empty??
so my major equation how I can compare samples even in same group