SHRiMP aligner options for unaligned (unmapped) reads

[bioWizz]

I am trying to align small RNA reads using SHRiMP using the command below

$ SHRiMP_2_2_3/bin/gmapper-ls -N 2 -o 1 -E input.fasta reference.fasta > output.sam

This gives me the .sam file output of only aligned reads. I also want the file containing unaligned reads. I saw the documentation and found the options

Output Control
--------------

  [ -E/--sam ]    Select SAM output format.

  [ --sam-unaligned ]    If SAM output format is also selected dump unaligned reads to the SAM output.

  [ -un <filename> ]    Print unaligned reads to target file.

  [ -al <filename> ]    Print aligned reads to target file.

I have tried using these parameters but have ended up obtaining blank files. Can anyone please guide me on the modification of my existing script to incorporate these parameters to get the unaligned output.

Thank you