OrthoFinder
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davidemms
orthofinder installation error on mac
i have installed orthofinder by conda orthofinder -hOrthoFinder version 2.4.0 Copyright (C) 2014 David Emms
SIMPLE USAGE: Run full OrthoFinder analysis on FASTA format proteomes in
Add new species in
OPTIONS:
-t
WORKFLOW STOPPING OPTIONS: -op Stop after preparing input files for BLAST -og Stop after inferring orthogroups -os Stop after writing sequence files for orthogroups (requires '-M msa') -oa Stop after inferring alignments for orthogroups (requires '-M msa') -ot Stop after inferring gene trees for orthogroups
WORKFLOW RESTART COMMANDS: -b
LICENSE: Distributed under the GNU General Public License (GPLv3). See License.md
CITATION: When publishing work that uses OrthoFinder please cite: Emms D.M. & Kelly S. (2019), Genome Biology 20:238
If you use the species tree in your work then please also cite: Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278 Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914 Traceback (most recent call last): File "/Users/padana/opt/anaconda3/bin/scripts_of/main.py", line 1678, in main ptm_initialised = parallel_task_manager.ParallelTaskManager_singleton() File "/Users/padana/opt/anaconda3/bin/scripts_of/parallel_task_manager.py", line 321, in init ParallelTaskManager_singleton.instance = ParallelTaskManager_singleton.__Singleton() File "/Users/padana/opt/anaconda3/bin/scripts_of/parallel_task_manager.py", line 316, in init self.manager_process.start() File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 224, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/context.py", line 284, in _Popen return Popen(process_obj) File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init super().init(process_obj) File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init self._launch(process_obj) File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 42, in _launch prep_data = spawn.get_preparation_data(process_obj._name) File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/spawn.py", line 154, in get_preparation_data _check_not_importing_main() File "/Users/padana/opt/anaconda3/lib/python3.9/multiprocessing/spawn.py", line 134, in _check_not_importing_main raise RuntimeError(''' RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
Anybody can guide me, what is the problem??
I am having the same issue. macOS Big Sur v11.3.1 and python 3.9.12. Orthofinder installation was through Bioconda.
Update: I was able to get around the problem using the docker. Below are the commands brew install --cask docker docker pull davidemms/orthofinder:2.5.4 docker run -it --rm davidemms/orthofinder:2.5.4 orthofinder -h docker run --ulimit nofile=1000000:1000000 -it --rm -v /full/path/to/fastas:/input:Z davidemms/orthofinder:2.5.4 orthofinder -f /input
