FastTree failed

[CongLiu37]

Hello,

I am trying to run orthofinder. Here is my command: orthofinder.py -f . -t 64 -M msa -A mafft -T fasttree and here is the output:

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-07-29 17:04:12 : Starting OrthoFinder 2.5.4
64 thread(s) for highly parallel tasks (BLAST searches etc.)
8 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - ok
Test can run "mafft OrthoFinder/OrthoFinder/Results_Jul29/WorkingDirectory//_dependencies_check/SimpleTest.fa" - ok
Test can run "FastTree OrthoFinder/OrthoFinder/Results_Jul29/WorkingDirectory//_dependencies_check/SimpleTest.fa" - failed

stdout:

stderr:
b'/bin/sh: FastTree: command not found\n'
ERROR: Cannot run FastTree
Please check FastTree is installed and that the executables are in the system path

Dependencies have been met for inference of orthogroups but not for the subsequent orthologue inference.
Either install the required dependencies or use the option '-og' to stop the analysis after the inference of orthogroups.

ERROR: An error occurred, ***please review the error messages*** they may contain useful information about the problem.

FastTree version 2.1.11 has been installed in my system, but its command is fasttree and command fasttree OrthoFinder/OrthoFinder/Results_Jul29/WorkingDirectory//_dependencies_check/SimpleTest.fa seems run without error.

Sincerely,

Cong Liu

[eskutkaan]

I solved this issue with the following steps;

1. Download setup.py from the source package. Or clone the source.
2. Because I don't have sudo rights, python3 setup.py install --user.
3. Step2 creates executable orthofinder in the folder /home/[username]/.local/bin/
4. Make sure that you have /home/[username]/.local/bin/ in your PATH.
5. Then copy all required executables into /home/[username]/.local/bin/ where orthofinder is installed.
6. Then you can use 'orthofinder' command directly. Not the .py

This solved it for me. I'm running it on an HPC. For some reason, nodes couldn't find the executables in my PATH.