Comments (12)
mortonjt
commented on June 3, 2024
Hi, something seems off with your tmvec install. It should be v1.0.2
…On Wed, Nov 1, 2023 at 5:46 AM Zjianglin ***@***.***> wrote:
Dear developers, I encountered a "Error" after installing deepblast
through python venv and pip:
Here is the error output:
(tmvec)$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
(tmvec)$ $ tmvec-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/tmvec-search", line 130, in <module>
args = parser.parse_args()
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 1826, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 1859, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 2068, in _parse_known_args
start_index = consume_optional(start_index)
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 2008, in consume_optional
take_action(action, args, option_string)
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 1936, in take_action
action(self, namespace, argument_values, option_string)
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 1099, in __call__
parser.print_help()
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 2556, in print_help
self._print_message(self.format_help(), file)
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 2540, in format_help
return formatter.format_help()
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 283, in format_help
help = self._root_section.format_help()
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 214, in format_help
item_help = join([func(*args) for func, args in self.items])
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 214, in <listcomp>
item_help = join([func(*args) for func, args in self.items])
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 214, in format_help
item_help = join([func(*args) for func, args in self.items])
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 214, in <listcomp>
item_help = join([func(*args) for func, args in self.items])
File "/lustre/home/zhoujianglin/.conda/envs/zjlEnv/lib/python3.10/argparse.py", line 532, in _format_action
if action.help and action.help.strip():
AttributeError: 'tuple' object has no attribute 'strip'
```
reproduce processes:
```
~/.conda/envs/xEnv/bin/python3 -m venv tmvec
source tmvec/bin/activate
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
pip install faiss-cpu
pip install -i https://pypi.tuna.tsinghua.edu.cn/simple tm-vec
```
Here is the systeminfo:
```
1. computer clusters (/lustre)
2. CentOS Linux release 7.9.2009 (Core)
3. $ pip list | egrep -i "blast|tm|cuda|py"
absl-py 2.0.0
biopython 1.81
contourpy 1.1.1
deepblast 1.0.1
MMPBSA.py 16.0
numpy 1.24.1
pyasn1 0.5.0
pyasn1-modules 0.3.0
pyMSMT 20.0
pyparsing 3.1.1
python-dateutil 2.8.2
pytorch-lightning 2.1.0
pytraj 2.0.6
pytz 2023.3.post1
PyYAML 6.0.1
scipy 1.11.3
sympy 1.12
tm-vec 1.0.1
```
Could you plseae help me figure it out? Thanks.
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from deepblast.
Zjianglin
commented on June 3, 2024
Hi @motonit, I using 'pip/search' to search the tm-vec and deepblast, but the lastest version is v1.0.1,see below:
tm-vec in pypi.org
deepblast in pypi.com
Then I tried to download the lastest version of deepblast from https://github.com/flatironinstitute/deepblast/releases, but the package still is v1.0.1 in setup.py. pip install . installed deepblast still is v1.0.1.
#setup.py from https://codeload.github.com/flatironinstitute/deepblast/tar.gz/refs/tags/1.0.2
setup(name='deepblast',
version='1.0.1',
license='BSD-3-Clause',
description=description,
author_email="[email protected]",
maintainer_email="[email protected]",
packages=find_packages(),
install_requires=[
'numpy',
'scipy',
'pandas',
'torch>=1.4',
'scikit-learn',
'numba',
'pytorch-lightning>=0.8.1',
'matplotlib',
'pillow',
'biopython>=1.78,<2.0',
'transformers',
'sentencepiece',
'tensorboard'
],
scripts=glob('scripts/*'),
classifiers=classifiers,
)
$ pip install -i https://pypi.tuna.tsinghua.edu.cn/simple .
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Processing /lustre/home/zhoujianglin/softwares/deepblast-1.0.2
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.26.1)
Requirement already satisfied: scipy in /lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.11.3)
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Building wheels for collected packages: deepblast
Building wheel for deepblast (setup.py) ... done
Created wheel for deepblast: filename=deepblast-1.0.1-py3-none-any.whl size=60343 sha256=422d01c0e40b64379f9cdfb07069381746cf90850768364bf1bd232945963319
Stored in directory: /lustre/home/zhoujianglin/.cache/pip/wheels/d4/62/85/6b306b41dab1088c956aac97b6d91a1ad3a3cf67814f8fe8cd
Successfully built deepblast
Installing collected packages: sentencepiece, pytz, mpmath, tzdata, typing-extensions, tqdm, threadpoolctl, tensorboard-data-server, sympy, safetensors, regex, PyYAML, pyparsing, pyasn1, protobuf, pillow, oauthlib, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, networkx, multidict, MarkupSafe, markdown, llvmlite, kiwisolver, joblib, grpcio, fsspec, frozenlist, fonttools, filelock, cycler, contourpy, cachetools, biopython, attrs, async-timeout, absl-py, yarl, werkzeug, triton, scikit-learn, rsa, requests-oauthlib, pyasn1-modules, pandas, nvidia-cusparse-cu12, nvidia-cudnn-cu12, numba, matplotlib, lightning-utilities, jinja2, huggingface-hub, aiosignal, tokenizers, nvidia-cusolver-cu12, google-auth, aiohttp, transformers, torch, google-auth-oauthlib, torchmetrics, tensorboard, pytorch-lightning, deepblast
Successfully installed MarkupSafe-2.1.3 PyYAML-6.0.1 absl-py-2.0.0 aiohttp-3.8.6 aiosignal-1.3.1 async-timeout-4.0.3 attrs-23.1.0 biopython-1.81 cachetools-5.3.2 contourpy-1.1.1 cycler-0.12.1 deepblast-1.0.1 filelock-3.13.1 fonttools-4.43.1 frozenlist-1.4.0 fsspec-2023.10.0 google-auth-2.23.4 google-auth-oauthlib-1.1.0 grpcio-1.59.2 huggingface-hub-0.17.3 jinja2-3.1.2 joblib-1.3.2 kiwisolver-1.4.5 lightning-utilities-0.9.0 llvmlite-0.41.1 markdown-3.5.1 matplotlib-3.8.1 mpmath-1.3.0 multidict-6.0.4 networkx-3.2.1 numba-0.58.1 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.18.1 nvidia-nvjitlink-cu12-12.3.52 nvidia-nvtx-cu12-12.1.105 oauthlib-3.2.2 pandas-2.1.2 pillow-10.1.0 protobuf-4.23.4 pyasn1-0.5.0 pyasn1-modules-0.3.0 pyparsing-3.1.1 pytorch-lightning-2.1.0 pytz-2023.3.post1 regex-2023.10.3 requests-oauthlib-1.3.1 rsa-4.9 safetensors-0.4.0 scikit-learn-1.3.2 sentencepiece-0.1.99 sympy-1.12 tensorboard-2.15.0 tensorboard-data-server-0.7.2 threadpoolctl-3.2.0 tokenizers-0.14.1 torch-2.1.0 torchmetrics-1.2.0 tqdm-4.66.1 transformers-4.34.1 triton-2.1.0 typing-extensions-4.8.0 tzdata-2023.3 werkzeug-3.0.1 yarl-1.9.2
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) [zhoujianglin@master deepblast-1.0.2]$ pip list | egrep -i "blast|tm|cuda"
deepblast 1.0.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) [zhoujianglin@master deepblast-1.0.2]$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
from deepblast.
mortonjt
commented on June 3, 2024
Its not deepblast that is the problem, it’s tmvec.
Try installing the dev version first
pip install git+
https://github.com/tymor22/tm-vec
And see if the tmvec version is up to date (v1.0.2).
It looks like the pypi version is dated — we’ll need to fix that
…On Wed, Nov 1, 2023 at 11:39 PM Zjianglin ***@***.***> wrote:
Hi @motonit, I using 'pip/search' to search the tm-vec and deepblast, but
the lastest version is v1.0.1,see below:
tm-vec in pypi.org <https://pypi.org/project/tm-vec/>
deepblast in pypi.com <https://pypi.org/project/deepblast/>
Then I tried to download the lastest version of deepblast from
https://github.com/flatironinstitute/deepblast/releases, but the package
still is v1.0.1 in setup.py. pip install . installed deepblast still is
v1.0.1.
etup(name='deepblast',
version='1.0.1',
license='BSD-3-Clause',
description=description,
***@***.***",
***@***.***",
packages=find_packages(),
install_requires=[
'numpy',
'scipy',
'pandas',
'torch>=1.4',
'scikit-learn',
'numba',
'pytorch-lightning>=0.8.1',
'matplotlib',
'pillow',
'biopython>=1.78,<2.0',
'transformers',
'sentencepiece',
'tensorboard'
],
scripts=glob('scripts/*'),
classifiers=classifiers,
)
$ pip install -i https://pypi.tuna.tsinghua.edu.cn/simple .
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Processing /lustre/home/zhoujianglin/softwares/deepblast-1.0.2
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.26.1)
Requirement already satisfied: scipy in /lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.11.3)
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Collecting sentencepiece
Downloading https://pypi.tuna.tsinghua.edu.cn/packages/7f/e5/323dc813b3e1339305f888d035e2f3725084fc4dcf051995b366dd26cc90/sentencepiece-0.1.99-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)
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Collecting lightning-utilities>=0.8.0
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Building wheels for collected packages: deepblast
Building wheel for deepblast (setup.py) ... done
Created wheel for deepblast: filename=deepblast-1.0.1-py3-none-any.whl size=60343 sha256=422d01c0e40b64379f9cdfb07069381746cf90850768364bf1bd232945963319
Stored in directory: /lustre/home/zhoujianglin/.cache/pip/wheels/d4/62/85/6b306b41dab1088c956aac97b6d91a1ad3a3cf67814f8fe8cd
Successfully built deepblast
Installing collected packages: sentencepiece, pytz, mpmath, tzdata, typing-extensions, tqdm, threadpoolctl, tensorboard-data-server, sympy, safetensors, regex, PyYAML, pyparsing, pyasn1, protobuf, pillow, oauthlib, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, networkx, multidict, MarkupSafe, markdown, llvmlite, kiwisolver, joblib, grpcio, fsspec, frozenlist, fonttools, filelock, cycler, contourpy, cachetools, biopython, attrs, async-timeout, absl-py, yarl, werkzeug, triton, scikit-learn, rsa, requests-oauthlib, pyasn1-modules, pandas, nvidia-cusparse-cu12, nvidia-cudnn-cu12, numba, matplotlib, lightning-utilities, jinja2, huggingface-hub, aiosignal, tokenizers, nvidia-cusolver-cu12, google-auth, aiohttp, transformers, torch, google-auth-oauthlib, torchmetrics, tensorboard, pytorch-lightning, deepblast
Successfully installed MarkupSafe-2.1.3 PyYAML-6.0.1 absl-py-2.0.0 aiohttp-3.8.6 aiosignal-1.3.1 async-timeout-4.0.3 attrs-23.1.0 biopython-1.81 cachetools-5.3.2 contourpy-1.1.1 cycler-0.12.1 deepblast-1.0.1 filelock-3.13.1 fonttools-4.43.1 frozenlist-1.4.0 fsspec-2023.10.0 google-auth-2.23.4 google-auth-oauthlib-1.1.0 grpcio-1.59.2 huggingface-hub-0.17.3 jinja2-3.1.2 joblib-1.3.2 kiwisolver-1.4.5 lightning-utilities-0.9.0 llvmlite-0.41.1 markdown-3.5.1 matplotlib-3.8.1 mpmath-1.3.0 multidict-6.0.4 networkx-3.2.1 numba-0.58.1 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.18.1 nvidia-nvjitlink-cu12-12.3.52 nvidia-nvtx-cu12-12.1.105 oauthlib-3.2.2 pandas-2.1.2 pillow-10.1.0 protobuf-4.23.4 pyasn1-0.5.0 pyasn1-modules-0.3.0 pyparsing-3.1.1 pytorch-lightning-2.1.0 pytz-2023.3.post1 regex-2023.10.3 requests-oauthlib-1.3.1 rsa-4.9 safetensors-0.4.0 scikit-learn-1.3.2 sentencepiece-0.1.99 sympy-1.12 tensorboard-2.15.0 tensorboard-data-server-0.7.2 threadpoolctl-3.2.0 tokenizers-0.14.1 torch-2.1.0 torchmetrics-1.2.0 tqdm-4.66.1 transformers-4.34.1 triton-2.1.0 typing-extensions-4.8.0 tzdata-2023.3 werkzeug-3.0.1 yarl-1.9.2
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) ***@***.*** deepblast-1.0.2]$ pip list | egrep -i "blast|tm|cuda"
deepblast 1.0.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) ***@***.*** deepblast-1.0.2]$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
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from deepblast.
Zjianglin
commented on June 3, 2024
Hi @mortonjt ， thanks for your timely reply. After install dev version tm-vec using pip install -i https://mirrors.sustech.edu.cn/pypi/simple git+https://github.com/tymor22/tm-vec, the tmvec-build-database -h and tmvec-search -h can now normally print out help messages. However, the installed versions of tm-vec and deepblast still is v1.0.1 as below:
$ pip list | egrep -i "blast|tm|cuda"
deepblast 1.0.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
tm-vec 1.0.1
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) [zhoujianglin@master softwares]$ tmvec-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
usage: tmvec-search [-h] --query QUERY --database DATABASE [--database-fasta DATABASE_FASTA] [--database-faidx DATABASE_FAIDX]
[--metadata METADATA] --tm-vec-model TM_VEC_MODEL --tm-vec-config TM_VEC_CONFIG [--deepblast-model DEEPBLAST_MODEL]
[--protrans-model PROTRANS_MODEL] [--device DEVICE] [--threads THREADS] [--alignment-mode ALIGNMENT_MODE]
[--k-nearest-neighbors K_NEAREST_NEIGHBORS] [--output-format OUTPUT_FORMAT] --output OUTPUT
[--output-embeddings OUTPUT_EMBEDDINGS]
Process TM-Vec arguments
options:
-h, --help show this help message and exit
--query QUERY Input fasta-formatted data to query against database.
--database DATABASE Database to query
--database-fasta DATABASE_FASTA
Database that contains the corresponding protein sequences in fasta format.
--database-faidx DATABASE_FAIDX
Fasta index for database fasta format.
--metadata METADATA Metadata for queried database
--tm-vec-model TM_VEC_MODEL
Model path for embedding
--tm-vec-config TM_VEC_CONFIG
Config path for embedding
--deepblast-model DEEPBLAST_MODEL
DeepBLAST model path
--protrans-model PROTRANS_MODEL
Model path for the ProTrans embedding model. If this is not specified, then the model will automatically be
downloaded.
--device DEVICE The device id to load the model onto. This will specify whether or not a GPU will be utilized. If `gpu` is specified
then the first gpu device will be used.
--threads THREADS Number of threads to use for parallel processing.
--alignment-mode ALIGNMENT_MODE
`smith-waterman` or `needleman-wunch`.
--k-nearest-neighbors K_NEAREST_NEIGHBORS
Number of nearest neighbhors to return for each query.
--output-format OUTPUT_FORMAT
Options include `tabular`, `alignment` or `embedding`.
--output OUTPUT Output search results.
--output-embeddings OUTPUT_EMBEDDINGS
Output encodings of query proteins (npy format).
I checked the setup.py of the (tm-vec repo)[https://github.com/tymor22/tm-vec/blob/master/setup.py], it still is setup(name='tm-vec', version='1.0.1', . And after installing using git+https...， the installed deepblast still is v1.0.1, and run into Error as before:
$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
Did I do something wrong or how should I fix this error? thanks.
from deepblast.
mortonjt
commented on June 3, 2024
Hi it looks like the problem is fixed. Looks like there was some issues
with the release - I’ll keep this open until the correct version is
displayed
…On Thu, Nov 2, 2023 at 4:51 AM Zjianglin ***@***.***> wrote:
Hi @mortonjt <https://github.com/mortonjt> ， thanks for your timely
reply. After install dev version tm-vec using pip install -i
https://mirrors.sustech.edu.cn/pypi/simple git+
https://github.com/tymor22/tm-vec, the tmvec-build-database -h and tmvec-search
-h can now normally print out help messages. However, the installed
versions of tm-vec and deepblast still is v1.0.1 as below:
$ pip list | egrep -i "blast|tm|cuda"
deepblast 1.0.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
tm-vec 1.0.1
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) ***@***.*** softwares]$ tmvec-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
usage: tmvec-search [-h] --query QUERY --database DATABASE [--database-fasta DATABASE_FASTA] [--database-faidx DATABASE_FAIDX]
[--metadata METADATA] --tm-vec-model TM_VEC_MODEL --tm-vec-config TM_VEC_CONFIG [--deepblast-model DEEPBLAST_MODEL]
[--protrans-model PROTRANS_MODEL] [--device DEVICE] [--threads THREADS] [--alignment-mode ALIGNMENT_MODE]
[--k-nearest-neighbors K_NEAREST_NEIGHBORS] [--output-format OUTPUT_FORMAT] --output OUTPUT
[--output-embeddings OUTPUT_EMBEDDINGS]
Process TM-Vec arguments
options:
-h, --help show this help message and exit
--query QUERY Input fasta-formatted data to query against database.
--database DATABASE Database to query
--database-fasta DATABASE_FASTA
Database that contains the corresponding protein sequences in fasta format.
--database-faidx DATABASE_FAIDX
Fasta index for database fasta format.
--metadata METADATA Metadata for queried database
--tm-vec-model TM_VEC_MODEL
Model path for embedding
--tm-vec-config TM_VEC_CONFIG
Config path for embedding
--deepblast-model DEEPBLAST_MODEL
DeepBLAST model path
--protrans-model PROTRANS_MODEL
Model path for the ProTrans embedding model. If this is not specified, then the model will automatically be
downloaded.
--device DEVICE The device id to load the model onto. This will specify whether or not a GPU will be utilized. If `gpu` is specified
then the first gpu device will be used.
--threads THREADS Number of threads to use for parallel processing.
--alignment-mode ALIGNMENT_MODE
`smith-waterman` or `needleman-wunch`.
--k-nearest-neighbors K_NEAREST_NEIGHBORS
Number of nearest neighbhors to return for each query.
--output-format OUTPUT_FORMAT
Options include `tabular`, `alignment` or `embedding`.
--output OUTPUT Output search results.
--output-embeddings OUTPUT_EMBEDDINGS
Output encodings of query proteins (npy format).
I checked the setup.py of the (tm-vec repo)[
https://github.com/tymor22/tm-vec/blob/master/setup.py], it still is setup(name='tm-vec',
version='1.0.1', . And after installing using git+https...， the installed
deepblast still is v1.0.1, and run into Error as before:
$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
Did I do something wrong or how should I fix this error? thanks.
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Zjianglin
commented on June 3, 2024
Hi, tm-vec seems OK now, but the deepblast still broken as error in `ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer'.
I'm downloading Prot-T5-XL-UniRef50 model weights of tm-vec and test it later. If you have any idea about solving the problem of deepblast, please help me. Thanks!
`
from deepblast.
mortonjt
commented on June 3, 2024
Hmm, the pypi version may also be off. Try
pip install git+
https://github.com/flatironinstitute/deepblast
…On Thu, Nov 2, 2023 at 4:51 AM Zjianglin ***@***.***> wrote:
Hi @mortonjt <https://github.com/mortonjt> ， thanks for your timely
reply. After install dev version tm-vec using pip install -i
https://mirrors.sustech.edu.cn/pypi/simple git+
https://github.com/tymor22/tm-vec, the tmvec-build-database -h and tmvec-search
-h can now normally print out help messages. However, the installed
versions of tm-vec and deepblast still is v1.0.1 as below:
$ pip list | egrep -i "blast|tm|cuda"
deepblast 1.0.1
nvidia-cuda-cupti-cu12 12.1.105
nvidia-cuda-nvrtc-cu12 12.1.105
nvidia-cuda-runtime-cu12 12.1.105
tm-vec 1.0.1
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
(tmvec) ***@***.*** softwares]$ tmvec-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
usage: tmvec-search [-h] --query QUERY --database DATABASE [--database-fasta DATABASE_FASTA] [--database-faidx DATABASE_FAIDX]
[--metadata METADATA] --tm-vec-model TM_VEC_MODEL --tm-vec-config TM_VEC_CONFIG [--deepblast-model DEEPBLAST_MODEL]
[--protrans-model PROTRANS_MODEL] [--device DEVICE] [--threads THREADS] [--alignment-mode ALIGNMENT_MODE]
[--k-nearest-neighbors K_NEAREST_NEIGHBORS] [--output-format OUTPUT_FORMAT] --output OUTPUT
[--output-embeddings OUTPUT_EMBEDDINGS]
Process TM-Vec arguments
options:
-h, --help show this help message and exit
--query QUERY Input fasta-formatted data to query against database.
--database DATABASE Database to query
--database-fasta DATABASE_FASTA
Database that contains the corresponding protein sequences in fasta format.
--database-faidx DATABASE_FAIDX
Fasta index for database fasta format.
--metadata METADATA Metadata for queried database
--tm-vec-model TM_VEC_MODEL
Model path for embedding
--tm-vec-config TM_VEC_CONFIG
Config path for embedding
--deepblast-model DEEPBLAST_MODEL
DeepBLAST model path
--protrans-model PROTRANS_MODEL
Model path for the ProTrans embedding model. If this is not specified, then the model will automatically be
downloaded.
--device DEVICE The device id to load the model onto. This will specify whether or not a GPU will be utilized. If `gpu` is specified
then the first gpu device will be used.
--threads THREADS Number of threads to use for parallel processing.
--alignment-mode ALIGNMENT_MODE
`smith-waterman` or `needleman-wunch`.
--k-nearest-neighbors K_NEAREST_NEIGHBORS
Number of nearest neighbhors to return for each query.
--output-format OUTPUT_FORMAT
Options include `tabular`, `alignment` or `embedding`.
--output OUTPUT Output search results.
--output-embeddings OUTPUT_EMBEDDINGS
Output encodings of query proteins (npy format).
I checked the setup.py of the (tm-vec repo)[
https://github.com/tymor22/tm-vec/blob/master/setup.py], it still is setup(name='tm-vec',
version='1.0.1', . And after installing using git+https...， the installed
deepblast still is v1.0.1, and run into Error as before:
$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
Did I do something wrong or how should I fix this error? thanks.
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You are receiving this because you were mentioned.Message ID:
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from deepblast.
Zjianglin
commented on June 3, 2024
Hi, sorry to bother you again. I uninstalled the previous deepblast and reinstalled it using 'pip install git+https:...' as below:
(tmvec) (base) [zhoujianglin@master softwares]$ pip install git+https://github.com/flatironinstitute/deepblast.git;
Collecting git+https://github.com/flatironinstitute/deepblast.git
Cloning https://github.com/flatironinstitute/deepblast.git to /tmp/pip-req-build-dojhyzpv
Running command git clone --quiet https://github.com/flatironinstitute/deepblast.git /tmp/pip-req-build-dojhyzpv
Resolved https://github.com/flatironinstitute/deepblast.git to commit 100085b92e73124dd110e13127f3d3a878286421
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.26.1)
Requirement already satisfied: scipy in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.11.3)
Requirement already satisfied: pandas in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (2.1.2)
Requirement already satisfied: torch>=1.4 in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (2.1.0)
Requirement already satisfied: scikit-learn in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.3.2)
Requirement already satisfied: numba in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (0.58.1)
Requirement already satisfied: pytorch-lightning>=0.8.1 in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (2.1.0)
Requirement already satisfied: matplotlib in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (3.8.0)
Requirement already satisfied: pillow in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (10.1.0)
Requirement already satisfied: biopython<2.0,>=1.78 in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (1.81)
Requirement already satisfied: transformers in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (4.34.1)
Requirement already satisfied: sentencepiece in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (0.1.99)
Requirement already satisfied: tensorboard in ./tmvec/lib/python3.10/site-packages (from deepblast==1.0.1) (2.15.0)
Requirement already satisfied: tqdm>=4.57.0 in ./tmvec/lib/python3.10/site-packages (from pytorch-lightning>=0.8.1->deepblast==1.0.1) (4.66.1)
Requirement already satisfied: PyYAML>=5.4 in ./tmvec/lib/python3.10/site-packages (from pytorch-lightning>=0.8.1->deepblast==1.0.1) (6.0.1)
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Requirement already satisfied: torchmetrics>=0.7.0 in ./tmvec/lib/python3.10/site-packages (from pytorch-lightning>=0.8.1->deepblast==1.0.1) (1.2.0)
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Requirement already satisfied: sympy in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (1.12)
Requirement already satisfied: networkx in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (3.2.1)
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Requirement already satisfied: nvidia-cuda-runtime-cu12==12.1.105 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (12.1.105)
Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (12.1.105)
Requirement already satisfied: nvidia-cudnn-cu12==8.9.2.26 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (8.9.2.26)
Requirement already satisfied: nvidia-cublas-cu12==12.1.3.1 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (12.1.3.1)
Requirement already satisfied: nvidia-cufft-cu12==11.0.2.54 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (11.0.2.54)
Requirement already satisfied: nvidia-curand-cu12==10.3.2.106 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (10.3.2.106)
Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (11.4.5.107)
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Requirement already satisfied: nvidia-nccl-cu12==2.18.1 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (2.18.1)
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Requirement already satisfied: triton==2.1.0 in ./tmvec/lib/python3.10/site-packages (from torch>=1.4->deepblast==1.0.1) (2.1.0)
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Requirement already satisfied: contourpy>=1.0.1 in ./tmvec/lib/python3.10/site-packages (from matplotlib->deepblast==1.0.1) (1.1.1)
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Requirement already satisfied: pyparsing>=2.3.1 in ./tmvec/lib/python3.10/site-packages (from matplotlib->deepblast==1.0.1) (3.1.1)
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Building wheels for collected packages: deepblast
Building wheel for deepblast (setup.py) ... done
Created wheel for deepblast: filename=deepblast-1.0.1-py3-none-any.whl size=60306 sha256=045c2c69edfd29f5fe47117f31eb4bf09685e0524f91869d2538e8753028dbf0
Stored in directory: /tmp/pip-ephem-wheel-cache-019gxxn8/wheels/ce/ee/2c/6a3383faecea59a1df6244c1ffd0c0dc9ba1565f2828af3a4b
Successfully built deepblast
Installing collected packages: deepblast
Successfully installed deepblast-1.0.1
(tmvec) (base) [zhoujianglin@master softwares]$ deepblast-search -h
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:487: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def is_subset(x, y):
/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/dataset/utils.py:499: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
def __trim_gap(x, k=10):
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.10/site-packages/deepblast/trainer.py)
It still broken.
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mortonjt
commented on June 3, 2024
Hi, I've updated pypi for both deepblast (v1.0.2) and tm-vec (v1.0.3). Feel free to reopen if you run into more issues.
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Zjianglin
commented on June 3, 2024
Hi, after reinstalling the tm-vec, their versions does updated as your description.
$ pip list | egrep -i "deep|tm"
deepblast 1.0.2
tm-vec 1.0.3
However, deepblast still can not be performed normally, Same Error as before:
$ deepblast-search -h
Traceback (most recent call last):
File "/lustre/home/zhoujianglin/softwares/tmvec/bin/deepblast-search", line 9, in <module>
from deepblast.trainer import LightningAligner
ImportError: cannot import name 'LightningAligner' from 'deepblast.trainer' (/lustre/home/zhoujianglin/softwares/tmvec/lib/python3.8/site-packages/deepblast/trainer.py)
(tmvec) (base) [zhoujianglin@master softwares]$ pip list | egrep -i "deep|python|tm"
biopython 1.81
deepblast 1.0.2
python-dateutil 2.8.2
tm-vec 1.0.3
(tmvec) (base) [zhoujianglin@master softwares]$ python --version
Python 3.8.15
Btw, I have tried python 3.10 and python 3.8, the same Error occured.
Here is my venv package version.
Uploading mytmvec_requir.txt…
Is there any problems with the installation process or do you have any solutions? Thanks.
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mortonjt
commented on June 3, 2024
ohhh I see, you are trying to run deepblast-search, which is deprecated (we need to remove that).
We recommend using tmvec-search instead as suggested in the wiki
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Zjianglin
commented on June 3, 2024
Ok, Thanks for your suggestion. I will learn it later. Thanks.
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Related Issues (20)
- No 'LightningAligner' can be import HOT 7
- Consistent usage of 'cuda' or 'gpu'
- Pass the device in load_model to Neural aligner HOT 1
- cannot import name 'LightningAligner' from 'deepblast.trainer' HOT 2
- DeepBLAST issue with model load HOT 3
- mat1 and mat2 must have the same dtype HOT 1
- Encountering an Issue While Building a Queryable Protein Sequence Database HOT 2
- Running time for searching query
- Running time for large query sequences HOT 1
- Smith-waterman test broken HOT 1
- Deepblast model confusion
- Where is the structure alignment output? HOT 2
- RuntimeError: The NVIDIA driver on your system is too old HOT 3
- After entering the command line, the program keeps running without any result. HOT 10
- Questions about evaluation metrics for sequence alignment HOT 4
- Unexpected keys in state_dict when I run this code on cpu HOT 3
- SW_cuda modual HOT 8
- TM-score calculation for DeepBlast HOT 4
- Feasible approach to build a large database HOT 1
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