If you are mapping an experiment from NCBI Sequence Read Archive, use -sra <accession> option:

magicblast -sra <accession> -db <database_name>

 

For example:

magicblast -sra SRR1237994 -db my_reference

 

To map several SRA runs use comma-separated list of accessions:

magicblast -sra SRR1237994,SRR1237993 -db my_reference

 

See Create BLAST database to see how to create a BLAST database.