Rainbow trout reference genome is available here. Rainbow trout chromosome number: 58 to 64
# Download the reference genome
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/163/495/GCF_002163495.1_Omyk_1.0/GCF_002163495.1_Omyk_1.0_genomic.fna.gz > GCF_002163495.1_Omyk_1.0_genomic.fna.gz
# Rename the file
mv gunzip GCF_002163495.1_Omyk_1.0_genomic.fna.gz.1 gunzip GCF_002163495.1_Omyk_1.0_genomic.fna.gz
# Unzip the file
gunzip GCF_002163495.1_Omyk_1.0_genomic.fna.gz
# Get one chromosome
mv GCF_002163495.1_Omyk_1.0_genomic.fna one_chromosome.fasta
# Index the genome, in this example case the chromosome
bwa index one_chromosome.fasta