Could not locate a Bowtie index corresponding to basename "rRNA"

The argument you are passing as the name of your reference is not the same as what you named it when you indexed it. Alternatively, you are not executing in the correct directory (i.e., providing the incorrect path).

Usage:
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.

Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
    reference_in            comma-separated list of files with ref sequences
    bt2_index_base          write bt2 data to files with this dir/basename
 Bowtie 2 indexes work only with v2 (not v1).  Likewise for v1 indexes.