AttributeError: 'Predictor' object has no attribute '__set_up_prodigal_thread'

[MrOlm]

Hello,

I'm trying to install checkM2 on my Mac with conda, but when I do the testrun I see the following:

$ checkm2 testrun
[02/27/2024 02:10:46 PM] INFO: Test run: Running quality prediction workflow on test genomes with 1 threads.
[02/27/2024 02:10:46 PM] INFO: Running checksum on test genomes.
[02/27/2024 02:10:46 PM] INFO: Checksum successful.
[02/27/2024 02:10:47 PM] INFO: Calling genes in 3 bins with 1 threads:
Traceback (most recent call last):
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "<string>", line 1, in <module>
  File "/Users/mattolm/miniconda3/envs/checkm2_drep/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
  File "/Users/mattolm/miniconda3/envs/checkm2_drep/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "/Users/mattolm/miniconda3/envs/checkm2_drep/lib/python3.8/multiprocessing/spawn.py", line 126, in _main
    exitcode = _main(fd, parent_sentinel)
  File "/Users/mattolm/miniconda3/envs/checkm2_drep/lib/python3.8/multiprocessing/spawn.py", line 126, in _main
    self = reduction.pickle.load(from_parent)
    self = reduction.pickle.load(from_parent)
AttributeError: 'Predictor' object has no attribute '__set_up_prodigal_thread'
AttributeError: 'Predictor' object has no attribute '__reportProgress'
[02/27/2024 02:11:04 PM] ERROR: Error: No protein files were generated in /var/folders/dx/80rf8pdn0j551086q04ftr340000gn/T/tmp3o7y_dk6/protein_files

Any ideas on how to fix?

Thanks, Matt

[jontang0]

I ran into this issue as well. I downgraded my version of python from 3.8 to 3.7 and it fixed this issue.

[rfour92]

I have the same problem on both testrun and actual MAGs. When I attempted to downgrade python from 3.8 to 3.7, conda was about to remove all dependencies. I couldn't find a way around it. can you kindly advise?

by the way, I am trying to install the tool using osx-64.

Just to clarify my machine is macbook M and the platform is osx-64 using rosetta