```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

# Run miRDeep2 mapping
time \
${mirdeep2_mapper} \
${concatenated_trimmed_reads_fasta_no_spaces} \
-c \
-m \
-l 18 \
-p ${genome_fasta_dir}/${genome_fasta_no_spaces%.*} \
-s ${collapsed_reads_gt17bp_mirdeep2} \
-t ${mirdeep2_mapping_file} \
-o ${threads}
```