Sometime functions will not run without -ri flag

[HectorBanos]

Need to check why somethings will not work without the -ri flag

for eg:

seq_Custom_UDM128_1.txt

meow -s /misc/scratch/hectorb/MEOW_uncover/seqs_128/seqs/seq_Custom_UDM128_1.phy -ch 40 -cl 20 -p R -f H -C 1e-10 -o MEOW4020_1Custom_UDM128_

[HectorBanos]

The problem is that the file has AA in lower case, which dgpe does not like, since in the process of the flag -ri the code rewrites the file without invariant sites, it fixes and changes it to upper case, which is why it runs with such a flag. Maybe it will be fixed that always rewrites an internal file with upper case, for now, avoid using lower case.