Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

"AttributeError: 'Parallel' object has no attribute '__process_manager" on GTDBTk v2.4.0 #619

Open
Thermosynechococcus opened this issue Jan 6, 2025 · 4 comments
Labels
error Help required for a GTDB-Tk error.

Comments

@Thermosynechococcus
Copy link

Thermosynechococcus commented Jan 6, 2025

I have installed GTDBTk ver 2.4.0. I am trying to classify MAGs by --classify_wf.
I have some problems and errors like this:

AttributeError: 'Parallel' object has no attribute '__process_manager'

Could anyone help me to solve it?
I have attached my command and the output.

gtdbtk classify_wf --genome_dir /Volumes/SSD/gtdbtk_input --out_dir OUT_DIR --skip_ani_screen
[2025-01-06 10:00:54] INFO: GTDB-Tk v2.4.0
[2025-01-06 10:00:54] INFO: gtdbtk classify_wf --genome_dir /Volumes/SSD/gtdbtk_input --out_dir OUT_DIR --skip_ani_screen
[2025-01-06 10:00:54] INFO: Using GTDB-Tk reference data version r220: /Volumes/SSD/gtdbtk_db
[2025-01-06 10:00:55] INFO: Identifying markers in 2 genomes with 1 threads.
[2025-01-06 10:00:55] TASK: Running Prodigal V2.6.3 to identify genes.
==> Processed 0/2 genomes (0%) | | [?geTraceback (most recent call last):
File "", line 1, in
File "/Users/XXX/opt/anaconda3/envs/gtdbtk-2.4.0/lib/python3.12/multiprocessing/spawn.py", line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/XXX/opt/anaconda3/envs/gtdbtk-2.4.0/lib/python3.12/multiprocessing/spawn.py", line 132, in _main
self = reduction.pickle.load(from_parent)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Parallel' object has no attribute '__process_manager'
Process Process-3:
[2025-01-06 10:02:51] ERROR: Controlled exit resulting from interrupt signal.
Process Process-2:
Traceback (most recent call last):

@Thermosynechococcus Thermosynechococcus added the error Help required for a GTDB-Tk error. label Jan 6, 2025
@Thermosynechococcus Thermosynechococcus changed the title "AttributeError: 'Parallel' object has no attribute '__process_manager" on GTDBTk ver2.4.0 "AttributeError: 'Parallel' object has no attribute '__process_manager" on GTDBTk v2.4.0 Jan 6, 2025
@Thermosynechococcus
Copy link
Author

The same error had been reported by
#366 (comment)

@pchaumeil
Copy link
Collaborator

Hello,
How did you install Tk? Which OS are you using? GTDB-Tk will not work on MacOS due to a third party dependency ( pplacer)

@Thermosynechococcus
Copy link
Author

Hi, thank you for reply.
my information is following,
Installation : conda
( I also tried insulation of Tk ver 2.1.1 using mamba, it reported the same error)
OS : Ventura 13.0.1
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5

@pchaumeil
Copy link
Collaborator

Hello,
As mentioned above, unfortunately GTDB-Tk will not on Ventura. One of the dependency,pplacer, is not supported in this OS. For this reason, We haven't tested GTDB-Tk on MacOS.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
error Help required for a GTDB-Tk error.
Projects
None yet
Development

No branches or pull requests

2 participants