Hi @Adyasha_Panda,
Can you provide more details? For example, what organisms are you interested in studying? I assume you are interested in 18S rRNA gene sequences / eukaryotes given that you're using SILVA and PR2? Which versions are you using?
Also, it is not uncommon to see differing taxonomic assignments between reference databases. This has been discussed several times on the forum. Here are at least two examples:
P.S. - We'll be adding the ability to automatically fetch and import the PR2 database into RESCRIPt soon.