Running ParaHunter.sh

[liamfriar]

Hi,

I am having trouble running ParaHunter. Running on Linux Ubuntu.

I set up using the instructions from the github.
git clone https://github.com/Arkadiy-Garber/ParaHunter.git cd ParaHunter bash setup.sh conda activate parahunt

I then try to run:
cd ~/tools/ParaHunter indir=~/data/find_plasmids/reference in_faa=Taz_complete.faa in_fna=Taz_complete.fna bash ParaHunter.sh -a ${indir}${in_faa} -n ${indir}/${in_fna}

And receive the following error:
ParaHunter.sh: line 61: fixfastas.py: command not found Clustering ORFs rm: cannot remove 'tmp/': No such file or directory rm: cannot remove 'clu': No such file or directory rm: cannot remove '*.index': No such file or directory rm: cannot remove '/home/liam/data/find_plasmids/referenceTaz_complete.faa.db': No such f ile or directory rm: cannot remove '/home/liam/data/find_plasmids/referenceTaz_complete.faa.db_h': No such file or directory rm: cannot remove '/home/liam/data/find_plasmids/referenceTaz_complete.faa.db.lookup': No such file or directory rm: cannot remove 'clu_seq.*': No such file or directory rm: cannot remove '/home/liam/data/find_plasmids/referenceTaz_complete.faa.db_h.dbtype': No such file or directory rm: cannot remove '/home/liam/data/find_plasmids/referenceTaz_complete.faa.db.source': No such file or directory mv: cannot stat 'clu.tsv': No such file or directory \033[0;32mSplitting ORFs into separate filescd g ParaHunter.sh: line 91: clu2fasta.py: command not found \033[0;32mPerforming dN/dS analysis with Codeml ParaHunter.sh: line 93: parahunter-dnds.py: command not found

If I try to call fixfastas.py on its own:
python fixfastas.py
I get
Traceback (most recent call last): File "/home/liam/tools/ParaHunter/fixfastas.py", line 385, in <module> nuc = open(args.nuc) FileNotFoundError: [Errno 2] No such file or directory: 'NA'
which indicates to me that fixfastas.py can be run.

I think this has something to do with the fact that I have to call
bash ParaHunter.sh
and
python fixfastas.py
while the examples on this github don't need the bash and then the call to fixfastas.py within ParaHunter.sh doesn't call python

[liamfriar]

Added ./ to the call to ParaHunter
so...
./ParaHunter.sh and also added ./ to the call to fixfastas.py from inside ParaHunter.sh
so ./fixfastas.py and now works.

[Arkadiy-Garber]

Hey Liam,

Thanks for the heads up on this! This is definitely how the software should behave. It sounds like parahunter.sh and fixfastas.py are not successfully added to your $PATH upon initialization of the conda env. I'll see what I can do to fix this.

Thanks!
Arkadiy

[Arkadiy-Garber]

Just updated the setup.sh script, so next time it is invoked, it should put the ParaHunter main directory in your $PATH.

For your system, I would recommend updating your .bash_profile or .profile files with the ParaHunter directory.

for example, paste a line that looks like this into one of these files:
PATH="$HOME/path/to/ParaHunter:$PATH"

Does this make sense?

Cheers,
Arkadiy

[liamfriar]

Hi Arakdiy,

We also had to chmod +x the other .py files and then add ./ in the ParaHunter.sh calls to them.

[liamfriar]

We are still running into trouble trying to run the package. Would currently be difficult for me to describe here as I am not sure where the problem is arising.

[Arkadiy-Garber]

Ok, feel free to email me