The rotate function not working

[tyler-peirce]

Hi Ian, I have been getting the new version of Emma running on Pawsey Setonix and it works when I do not use the --rotate function. When i add in --rotate MT-TF (also tested with MT-TM and get the same eroor) I am getting the following error:

@ Emma /opt/Emma/src/cmd.jl:115
ERROR: LoadError: BoundsError: attempt to access 0-element Vector{String} at index [1]
Stacktrace:
 [1] getindex(A::Vector{String}, i1::Int64)
   @ Base ./essentials.jl:13
 [2] top-level scope
   @ /opt/extract_proteins.jl:132
in expression starting at /opt/extract_proteins.jl:13

The code that I am running is as follows:

/opt/julia-1.10.5/bin/julia \
    /opt/Emma/src/command.jl \
    --rotate MT-TF \
    --fa emma/OG33.ilmn.240716.getorg1770.emma${emma_version}.fa \
    --gff emma/OG33.ilmn.240716.getorg1770.emma${emma_version}.fa.gff \
    --tbl emma/OG33.ilmn.240716.getorg1770.emma${emma_version}.tbl \
    --svg emma/OG33.ilmn.240716.getorg1770.emma${emma_version}.svg \
    --tempdir tempdir/ \
    OG33.ilmn.240716.getorg1770.animal_mt.K115.complete.graph1.1.path_sequence.fasta > OG33.ilmn.240716.getorg1770.emma${emma_version}.out.txt

I have also attached the full error output, it almost looks like the new rotated output is going into the error file instead.
error.txt

[ian-small]

Thanks, Tyler, for the bug report. This problem should be fixed now if you reinstall. Let me know if it works or not.