rtrp@rtrp-Inspiron-3420:/media/New Volume/Vel/mirdeep2$ perl mapper.pl config.txt -c -d -i -j -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -p rn5.index -s reads.fa -t reads_vs_genome.arf -v
handling file 'H9A2M.fasta' with prefix 'A2M'
converting rna to dna alphabet
sh: 1: rna2dna.pl: not found
discarding sequences with non-canonical letters
clipping 3' adapters
sh: 1: clip_adapters.pl: not found
discarding short reads
collapsing reads
sh: 1: collapse_reads_md.pl: not found
mapping reads to genome index