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$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
The text was updated successfully, but these errors were encountered:
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/]
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
The text was updated successfully, but these errors were encountered: