From manual (copy/pasted in parts):

For Indexing:

The executable indexdb rna indexes an rRNA database.

Example 1: indexdb rna using one database
>> ./indexdb_rna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db -v

usage: ./indexdb_rna --ref db.fasta,db.idx [OPTIONS]:
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| parameter          value          description             default |
--------------------------------------------------------------------------------------------------------
--ref              STRING,STRING      FASTA  reference file, index file        mandatory
(ex. --ref /path/to/file1.fasta,/path/to/index1)
If passing multiple reference sequence files, separate
them by ’:’,
(ex. --ref /path/to/file1.fasta,/path/to/index1:/path/to/file2.fasta,path/to/index2)

For sortmeRNA

usage: ./sortmerna --ref db.fasta,db.idx --reads file.fa --aligned base_name_output [OPTIONS]:
-------------------------------------------------------------------------------------------------------------
| parameter value description default |
-------------------------------------------------------------------------------------------------------------
--ref STRING,STRING FASTA reference file, index file mandatory
(ex. --ref /path/to/file1.fasta,/path/to/index1)
If passing multiple reference files, separate
them using the delimiter ’:’,
(ex. --ref /path/to/file1.fasta,/path/to/index1:/path/to/file2.fasta,path/to