New 2.6.1 version AttributeError: 'Parallel' object has no attribute '__process_manager'

[KennLu2914]

Hi Pierre,

Just updated to the new 2.6.1 version (installed by mamba), had a successful run on the first download, then it keeps going into the following error message on aqua server:

[2025-12-22 00:43:40] INFO: Using GTDB-Tk reference data version r226: /work/WISE_microbes/db/gtdb/release226/
[2025-12-22 00:43:40] INFO: Identifying markers in 58 genomes with 1 threads.
[2025-12-22 00:43:40] TASK: Running Prodigal V2.6.3 to identify genes.
==> Processed 0/58 genomes (0%) | | [?genome/s, ETA ?]Traceback (most recent call last):
File "/mnt/hpccs01/work/WISE_microbes/miniforge3/envs/gtdbtk/lib/python3.14/multiprocessing/forkserver.py", line 340, in main
code = _serve_one(child_r, fds,
unused_fds,
old_handlers)
File "/mnt/hpccs01/work/WISE_microbes/miniforge3/envs/gtdbtk/lib/python3.14/multiprocessing/forkserver.py", line 380, in _serve_one
code = spawn._main(child_r, parent_sentinel)
File "/mnt/hpccs01/work/WISE_microbes/miniforge3/envs/gtdbtk/lib/python3.14/multiprocessing/spawn.py", line 132, in _main
self = reduction.pickle.load(from_parent)
AttributeError: 'Parallel' object has no attribute '__process_manager'

Tried to update mamba and all packages.

Server information

• CPU: grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo
• model name : AMD EPYC 9684X 96-Core Processor
  384

Thank you

[ruben1294]

Hello, I had exactly the same error. Same version of python as well (3.14). From what I looked, it seems like python 3.14 is incompatible with GTDB-Tk 2.6.1, as it's very recent. You could try with an older version of python, I will try that in the next few weeks and see if that solves the issue. If you happen to try that, please let us know as well.

Some threads with similar issues that point to issues with parallel job of python 3.1X:

joblib/joblib#1544
pydantic/pydantic#12618

Kind regards,
Rubén

[Jiung-Wen]

I ran into the same issue and solved it by pinning Python to version 3.12.
mamba create -n gtdbtk-2.6.1 -c conda-forge -c bioconda gtdbtk=2.6.1 python=3.12
I haven't tested this with Python 3.13, as 3.12 worked for me. I hope this helps.

[KennLu2914]

Thanks @ruben1294 @Jiung-Wen, that works perfectly with Python 3.12.

Cheers

[fplazaonate]

It works with Python 3.13 as well.
I will update the bioconda recipe accordingly.

[fplazaonate]

It is fixed with the new bioconda recipe.
GTDB-tk is now installed with Python < 3.14