Automating busted in Hyphy
Entering edit mode
27 days ago
Rijan • 0

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):

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
    file_base="$(basename $file .pal)"
    echo `(echo "1"; echo "5"; echo $file; echo $treefile) | hyphy`

So, hyphy shows up on my resource usage tabs in linux. Look at the top item: enter image description here 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.

Hyphy phylogenetics. BUSTED • 91 views

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