How to align fastq files against a reference assembly

Hello,

I am trying to align fastq files against the bacterial MRSA ATCC 33591 reference genome. The problem I am facing is that I have the reference assembly in fasta format with multiple sequences and upon creating index with hisat2-build I am not getting a good alignment rate. In fact most of the reads go unaligned.

I am curious to know if hisat2 can be used with genome assemblies directly or it needs to be converted to a single fasta file? Or am I doing something wrong.

I am new with bacterial genome and any advice on what to do or which tools to use will be helpful.

Thank you.