BASH SortMeRNA--Fasta Must be followed by an index name

Question

[dcjordan128]

Help! I'm trying to submit a script to sort out rRNA contamination from my RNA-sequencing using SortMeRNA. I tried running the script but just got this error message back:

ESC[0;31mERRORESC[0m: the FASTA reference file name /uoa/home/r01dj21/Software/sortmerna/sortmerna-2.1b/rRNA_databases/silva-euk-18s-id95.fasta must be followed by an index name.

What is an index name and how do I enter that into my script? It wasn't in the original guidelines for SortMeRNA.

Thank you!

[cpad0112]

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]:
--------------------------------------------------------------------------------------------------------
| 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