So when I run this in Fedora I'm seeing this:
$ ls hmm_data/indivA12_AATAAG/refs/par1/
2R-orths.alleles 2R-ref.alleles
$ ls hmm_data/indivA12_AATAAG/refs/par1/ | grep -F '-ref.alleles'
2R-ref.alleles
But when I run on Ubuntu (same data) I don't get any results from the grep:
$ ls hmm_data/indivA12_AATAAG/refs/par1/
2R-orths.alleles 2R-ref.alleles
$ ls hmm_data/indivA12_AATAAG/refs/par1/ | grep -F '-ref.alleles'
Any ideas what could be going on? How can I come up with something that will work the same on both systems?