def TypedDict(typename, fields=_marker,/, *, total=True, closed=False, **kwargs): SyntaxError: invalid syntax

[zhaoxuetong]

Hello,

I have some errors with gtdbtk v2.1.0.

$gtdbtk check_install
Traceback (most recent call last):
File "/home/zhaoxt/.conda/envs/GTDB/bin/gtdbtk", line 6, in
from gtdbtk.main import main
File "/home/zhaoxt/.local/lib/python3.7/site-packages/gtdbtk-2.3.2-py3.7.egg/gtdbtk/main.py", line 27, in
from gtdbtk.files.stage_logger import StageLogger
File "/home/zhaoxt/.local/lib/python3.7/site-packages/gtdbtk-2.3.2-py3.7.egg/gtdbtk/files/stage_logger.py", line 5, in
from pydantic import BaseModel
File "pydantic/init.py", line 2, in init pydantic.init
File "pydantic/dataclasses.py", line 3, in init pydantic.dataclasses
import copy
File "pydantic/class_validators.py", line 8, in init pydantic.class_validators
File "pydantic/errors.py", line 5, in init pydantic.errors
File "pydantic/typing.py", line 25, in init pydantic.typing
import contextlib
File "/home/zhaoxt/.local/lib/python3.7/site-packages/typing_extensions-4.11.0-py3.7.egg/typing_extensions.py", line 958
def TypedDict(typename, fields=_marker,/, *, total=True, closed=False, **kwargs):
^
SyntaxError: invalid syntax

[pchaumeil]

Hi,
I do recommend using the last version of GTDB-Tk.

• If you would like to use R214 of GTDB, please install v2.3.2 of GTDB-Tk
• If you would like to use R220 of GTDB, please install v2.4.0 of GTDB-Tk

Regards,
Pierre

[zhaoxuetong]

Hi Pierre,

Thank you for your prompt reply.
I have a little question about environmental variables.
If my GTDB database R214 is downloaded to $(pwd)/GTDB_software/release214/, and my virtual environment name is gtdbtk-2.3.2, then which of the following is correct:
export GTDBTK_DATA_PATH=$(pwd)/GTDB_software/release214/
export GTDBTK_DATA_PATH=~/.conda/envs/gtdbtk-2.3.2/share/gtdbtk-2.3.2/db"

I'm a little confused now, I don't know if GTDB database R214 must be placed under ~/.conda/envs/gtdbtk-2.3.2/share/gtdbtk-2.3.2/db

Also I run gtdbtk check_install and wait for a long time in [$(pwd)/GTDB_software/release214/fastani/]

Thank you for your reply.
xuetong Zhao

[pchaumeil]

Hello,

• You don't have to place the GDTB-Tk database in the conda environment, you can store it anywhere you want on your server.
• gtdbtk check_install will take a long time at the FastANI as it checks the checksum of all 85K representative genomes of R214.