FAQ

For the core compilation step, fDOG will traverses a taxonomy tree to find and add new members to the core orthologous groups. This taxonomy tree is generated based on the NCBI taxonomy IDs of the species that are considered for the core compilation. These core taxa are the one that can be found in the coreTaxa_dir folder in the fDOG data directory.

For other steps, such as ortholog search or FAS score calculation, fDOG does not need the real NCBI taxonomy of the search taxa, as long as the user searches for orthologs in all the the species located in the searchTaxa_dir folder without limiting the search on any taxonomy rank.

Therefore, if you want to use fDOG for seaching orthologs in non-ncbi species, you can do that by putting all of your search taxa (doesn't matter if they have or don't have a valid NCBI taxonomy ID) in the searchTaxa_dir folder, and keep only core taxa that have NCBI IDs in the coreTaxa_dir folder.

Troubleshooting

Problems with Perl

(This is only the solution for Conda and only for fDOG < v0.1.0)

The Perl dependencies are installed to /home directory

Installing dependencies...

Can't write to /usr/local/share/perl/5.30.0 and /usr/local/bin: Installing modules to /home/ruben/perl5
To turn off this warning, you have to do one of the following:
  - run me as a root or with --sudo option (to install to /usr/local/share/perl/5.30.0 and /usr/local/bin)
  - Configure local::lib in your existing shell to set PERL_MM_OPT etc.
  - Install local::lib by running the following commands

        cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)

Successfully reinstalled Array-Utils-0.5

and then they cannot be loaded within the same conda environment using for installing them

Perl modules
	Array::Utils could not be installed
	DBI could not be installed
	File::Which could not be installed
	Parallel::ForkManager could not be installed
	Statistics::R could not be installed
	Bio::SearchIO::blastxml could not be installed
done!
Environment paths
done!
Some tools/libraries counld not installed correctly or paths were not added into ~/.bashrc.
Please manually install the missing dependencies using using fdog.setup with --lib option (ask your admin if you don't have root privileges).
Then run this setup again to try one more time!

If it is the case, you could follow these steps (thanks Rubén - @Yruegas):

Remove the sections that contain $HOME/.local in the line export PATH=... in your ~/.bashrc (or ~/.bash_profile)
Remove (should back them up before removing) the folder ~/.local/bin and ~/.local/lib. *Please be aware that some programs in those folders need to be reinstalled in the intended environment)
Remove (should back them up before removing) the folder ~/perl5
Create a conda environment with perl and python conda create -n fdog python=3.9 perl-env
Go to that environment and install cpanm conda install -c bioconda perl-app-cpanminus
Reinstall and do setup fDOG (and FAS if needed)
If perl module DBI cannot be installed because of the missing gcc, you can install it using conda install -c conda-forge gcc

These issues are temporary. We will soon remove perl dependencies from fDOG!

Problems with Python

Command not found

~$ fdog.setup
zsh: command not found: fdog.setup

This could probably be because you have different versions of Python and Pip on the computer, mostly happens on MacOS. The solution for this is either using Conda, or try to use pyenv to manage Python on your system. You can follow this short instruction to install and use pyenv.