Automating busted in Hyphy
0
0
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): 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: 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
ADD COMMENT

Login before adding your answer.

Traffic: 2754 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6