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

or a list of accessions in text file, one per line:

echo SRR1237994 >accessions
echo SRR1237993 >>accessions
magicblast -sra_batch accessions -db my_reference


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