```bash
# Load bash variables into memory
source .bashvars

# Move to output directory
# miRDeep2 puts output files in current working directory
cd ${output_dir_top}

# Append miRDeep2 to system PATH and set PERL5LIB
export PATH=$PATH:/home/shared/mirdeep2/bin
export PERL5LIB=$PERL5LIB:/home/shared/mirdeep2/lib/perl5

time \
${mirdeep2} \
${collapsed_reads_gt17bp_mirdeep2} \
${genome_fasta_dir}/${genome_fasta_no_spaces} \
${mirdeep2_mapping_file} \
none \
${deep_dive_data_dir}/${cnidarian_mirna_fasta_name} \
none \
-P \
-v \
-g -1 \
2>miRDeep2-report.log
```