I am trying to run BUSTED in hyphy on 129 ortho files and corresponding treefiles. So, running it interactively is not applicable here. I am trying to automate the runs over all of the files. I am using Hyphy installed from conda. I am using this manual web page as a reference to create a bash loop (scroll to the end of the webpage): https://stevenweaver.github.io/hyphy-site/tutorials/current-release-tutorial/.

The bash for loop that I came up with looks like this:

cd /home/opensourceferns/Desktop/map-multifile-cds-to-protein-alignment/hyphy/Test_run

for file  in *.pal
do
    file_base="$(basename $file .pal)"
    ext=".treefile"
    treefile="$file_base$ext"
    echo `(echo "1"; echo "5"; echo $file; echo $treefile) | hyphy`
done

So, hyphy shows up on my resource usage tabs in linux. Look at the top item: But the thing is the run has been going on for hours and there is no data. I have an empty error log file and an empty JSON file. This is a test run on one orthofiles and this one has 203 sequences in it. Did I set up the automation script wrong? I only want to run the input using default settings.