/usr/local/phylogeny/phyml/bin/phyml-codon.sh JTT-ML91+-0-e-F input_files/20200423_110259/input.phy 
is translated to
/usr/local/phylogeny/phyml/bin/phyml -i input_files/20200423_110259/input.phy -d codon -b 0 --mechanistic_opt 00000 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace
/usr/local/phylogeny/phyml/bin/phyml: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory