Hi @manojndsu,
Please have a careful look at the Moving Pictures tutorial again, right from the beginning.. It starts with downloading raw .fastq files and step by step shows how to go about developing all those intermediary files such as distance-matrix etc for downstream use. In your case you already have the .fastq files so you wouldn't be downloading anything. Your importing step might differ than the Moving Pictures tutorial, see the importing tutorial to find the method that matches your file format. Once you have your fastq files imported into QIIME 2, then you can resume following along the Moving Pictures tutorial which also has a step that shows when you would use a reference databases (example Greengenes or Silva).
Please read the tutorials carefully and let us know if you run into any specific problems.