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Graylab / IgFold

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
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Installation failure and IgFold cannot run on Google Colab #24

Closed WenTao-tust closed 1 year ago

WenTao-tust commented 1 year ago

I was unable to install IgFold on my computer after installing Anaconda following the installation steps you explained and have tried several times. Meanwhile，IgFold cannot run on Google Colab.

WenTao-tust commented 1 year ago

ModuleNotFoundError Traceback (most recent call last) /usr/local/lib/python3.7/site-packages/transformers/utils/import_utils.py in _get_module(self, module_name) 1092 try: -> 1093 return importlib.import_module("." + module_name, self.name) 1094 except Exception as e:

31 frames ModuleNotFoundError: No module named 'tokenizers.tokenizers'

The above exception was the direct cause of the following exception:

RuntimeError Traceback (most recent call last) /usr/local/lib/python3.7/site-packages/transformers/utils/import_utils.py in _get_module(self, module_name) 1093 return importlib.import_module("." + module_name, self.name) 1094 except Exception as e: -> 1095 raise RuntimeError( 1096 f"Failed to import {self.name}.{module_name} because of the following error (look up to see its" 1097 f" traceback):\n{e}"

RuntimeError: Failed to import transformers.models.auto because of the following error (look up to see its traceback): No module named 'tokenizers.tokenizers'

jeffreyruffolo commented 1 year ago

Hello, I'm wondering if it is an issue with dependency versions. Can you share some information about your local python environment? The output of pip list would be helpful.

WenTao-tust commented 1 year ago

The installation process is as follows：

pip install IgFold Collecting IgFold Using cached igfold-0.2.2-py3-none-any.whl (34 kB) Collecting tokenizers>=0.11.6 Using cached tokenizers-0.13.2-cp39-cp39-win_amd64.whl (3.3 MB) Collecting IgFold Using cached igfold-0.2.1-py3-none-any.whl (34 kB) Using cached igfold-0.2.0-py3-none-any.whl (34 kB) Using cached igfold-0.1.5-py3-none-any.whl (31 kB) Using cached igfold-0.1.4-py3-none-any.whl (31 kB) Using cached igfold-0.1.3-py3-none-any.whl (31 kB) Using cached igfold-0.1.2-py3-none-any.whl (31 kB) Using cached igfold-0.1.1-py3-none-any.whl (31 kB) Using cached igfold-0.1.0-py3-none-any.whl (31 kB) Using cached igfold-0.0.8-py3-none-any.whl (30 kB) Using cached igfold-0.0.7-py3-none-any.whl (30 kB) Using cached igfold-0.0.6-py3-none-any.whl (29 kB) Using cached igfold-0.0.5-py3-none-any.whl (28 kB) Using cached igfold-0.0.4-py3-none-any.whl (28 kB) ERROR: Cannot install igfold==0.0.4, igfold==0.0.5, igfold==0.0.6, igfold==0.0.7, igfold==0.0.8, igfold==0.1.0, igfold==0.1.1, igfold==0.1.2, igfold==0.1.3, igfold==0.1.4, igfold==0.1.5, igfold==0.2.0, igfold==0.2.1 and igfold==0.2.2 because these package versions have conflicting dependencies.

The conflict is caused by: igfold 0.2.2 depends on pytorch3d igfold 0.2.1 depends on pytorch3d igfold 0.2.0 depends on pytorch3d igfold 0.1.5 depends on pytorch3d igfold 0.1.4 depends on pytorch3d igfold 0.1.3 depends on pytorch3d igfold 0.1.2 depends on pytorch3d igfold 0.1.1 depends on pytorch3d igfold 0.1.0 depends on pytorch3d igfold 0.0.8 depends on pytorch3d igfold 0.0.7 depends on pytorch3d igfold 0.0.6 depends on pytorch3d igfold 0.0.5 depends on pytorch3d igfold 0.0.4 depends on pytorch3d

To fix this you could try to:

  1. loosen the range of package versions you've specified
  2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts

the pip list are as follow：

Package Version

alabaster 0.7.12 anaconda-client 1.11.0 anaconda-navigator 2.3.2 anaconda-project 0.11.1 anyio 3.5.0 appdirs 1.4.4 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 arrow 1.2.2 astroid 2.11.7 astropy 5.1 atomicwrites 1.4.0 attrs 21.4.0 Automat 20.2.0 autopep8 1.6.0 Babel 2.9.1 backcall 0.2.0 backports.functools-lru-cache 1.6.4 backports.tempfile 1.0 backports.weakref 1.0.post1 bcrypt 3.2.0 beautifulsoup4 4.11.1 binaryornot 0.4.4 bitarray 2.5.1 bkcharts 0.2 black 22.6.0 bleach 4.1.0 bokeh 2.4.3 boto3 1.24.28 botocore 1.27.28 Bottleneck 1.3.5 brotlipy 0.7.0 certifi 2022.9.14 cffi 1.15.1 chardet 4.0.0 charset-normalizer 2.0.4 click 8.0.4 cloudpickle 2.0.0 clyent 1.2.2 colorama 0.4.5 colorcet 3.0.0 comtypes 1.1.10 conda 22.11.1 conda-build 3.22.0 conda-content-trust 0.1.3 conda-pack 0.6.0 conda-package-handling 1.9.0 conda-repo-cli 1.0.20 conda-token 0.4.0 conda-verify 3.4.2 constantly 15.1.0 cookiecutter 1.7.3 cryptography 37.0.1 cssselect 1.1.0 cycler 0.11.0 Cython 0.29.32 cytoolz 0.11.0 daal4py 2021.6.0 dask 2022.7.0 datashader 0.14.1 datashape 0.5.4 debugpy 1.5.1 decorator 5.1.1 defusedxml 0.7.1 diff-match-patch 20200713 dill 0.3.4 distributed 2022.7.0 docutils 0.18.1 entrypoints 0.4 et-xmlfile 1.1.0 fastjsonschema 2.16.2 filelock 3.6.0 flake8 4.0.1 Flask 1.1.2 fonttools 4.25.0 fsspec 2022.7.1 future 0.18.2 gensim 4.1.2 glob2 0.7 greenlet 1.1.1 h5py 3.7.0 HeapDict 1.0.1 holoviews 1.15.0 hvplot 0.8.0 hyperlink 21.0.0 idna 3.3 imagecodecs 2021.8.26 imageio 2.19.3 imagesize 1.4.1 importlib-metadata 4.11.3 incremental 21.3.0 inflection 0.5.1 iniconfig 1.1.1 intake 0.6.5 intervaltree 3.1.0 ipykernel 6.15.2 ipython 7.31.1 ipython-genutils 0.2.0 ipywidgets 7.6.5 isort 5.9.3 itemadapter 0.3.0 itemloaders 1.0.4 itsdangerous 2.0.1 jdcal 1.4.1 jedi 0.18.1 jellyfish 0.9.0 Jinja2 2.11.3 jinja2-time 0.2.0 jmespath 0.10.0 joblib 1.1.0 json5 0.9.6 jsonschema 4.16.0 jupyter 1.0.0 jupyter_client 7.3.4 jupyter-console 6.4.3 jupyter_core 4.11.1 jupyter-server 1.18.1 jupyterlab 3.4.4 jupyterlab-pygments 0.1.2 jupyterlab-server 2.10.3 jupyterlab-widgets 1.0.0 keyring 23.4.0 kiwisolver 1.4.2 lazy-object-proxy 1.6.0 libarchive-c 2.9 llvmlite 0.38.0 locket 1.0.0 lxml 4.9.1 lz4 3.1.3 Markdown 3.3.4 MarkupSafe 2.0.1 matplotlib 3.5.2 matplotlib-inline 0.1.6 mccabe 0.6.1 menuinst 1.4.19 mistune 0.8.4 mkl-fft 1.3.1 mkl-random 1.2.2 mkl-service 2.4.0 mock 4.0.3 mpmath 1.2.1 msgpack 1.0.3 multipledispatch 0.6.0 munkres 1.1.4 mypy-extensions 0.4.3 navigator-updater 0.3.0 nbclassic 0.3.5 nbclient 0.5.13 nbconvert 6.4.4 nbformat 5.5.0 nest-asyncio 1.5.5 networkx 2.8.4 nltk 3.7 nose 1.3.7 notebook 6.4.12 numba 0.55.1 numexpr 2.8.3 numpy 1.21.5 numpydoc 1.4.0 olefile 0.46 openpyxl 3.0.10 packaging 21.3 pandas 1.4.4 pandocfilters 1.5.0 panel 0.13.1 param 1.12.0 paramiko 2.8.1 parsel 1.6.0 parso 0.8.3 partd 1.2.0 pathlib 1.0.1 pathspec 0.9.0 patsy 0.5.2 pep8 1.7.1 pexpect 4.8.0 pickleshare 0.7.5 Pillow 9.2.0 pip 22.2.2 pkginfo 1.8.2 platformdirs 2.5.2 plotly 5.9.0 pluggy 1.0.0 poyo 0.5.0 prometheus-client 0.14.1 prompt-toolkit 3.0.20 Protego 0.1.16 psutil 5.9.0 ptyprocess 0.7.0 py 1.11.0 pyasn1 0.4.8 pyasn1-modules 0.2.8 pycodestyle 2.8.0 pycosat 0.6.3 pycparser 2.21 pyct 0.4.8 pycurl 7.45.1 PyDispatcher 2.0.5 pydocstyle 6.1.1 pyerfa 2.0.0 pyflakes 2.4.0 Pygments 2.11.2 PyHamcrest 2.0.2 PyJWT 2.4.0 pylint 2.14.5 pyls-spyder 0.4.0 PyNaCl 1.5.0 pyodbc 4.0.34 pyOpenSSL 22.0.0 pyparsing 3.0.9 pyrsistent 0.18.0 PySocks 1.7.1 pytest 7.1.2 python-dateutil 2.8.2 python-lsp-black 1.0.0 python-lsp-jsonrpc 1.0.0 python-lsp-server 1.3.3 python-slugify 5.0.2 python-snappy 0.6.0 pytz 2022.1 pyviz-comms 2.0.2 PyWavelets 1.3.0 pywin32 302 pywin32-ctypes 0.2.0 pywinpty 2.0.2 PyYAML 6.0 pyzmq 23.2.0 QDarkStyle 3.0.2 qstylizer 0.1.10 QtAwesome 1.0.3 qtconsole 5.2.2 QtPy 2.2.0 queuelib 1.5.0 regex 2022.7.9 requests 2.28.1 requests-file 1.5.1 rope 0.22.0 Rtree 0.9.7 ruamel.yaml 0.17.21 ruamel.yaml.clib 0.2.6 ruamel-yaml-conda 0.15.100 s3transfer 0.6.0 scikit-image 0.19.2 scikit-learn 1.0.2 scikit-learn-intelex 2021.20221004.171935 scipy 1.9.1 Scrapy 2.6.2 seaborn 0.11.2 Send2Trash 1.8.0 service-identity 18.1.0 setuptools 63.4.1 sip 4.19.13 six 1.16.0 smart-open 5.2.1 sniffio 1.2.0 snowballstemmer 2.2.0 sortedcollections 2.1.0 sortedcontainers 2.4.0 soupsieve 2.3.1 Sphinx 5.0.2 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.5 spyder 5.2.2 spyder-kernels 2.2.1 SQLAlchemy 1.4.39 statsmodels 0.13.2 sympy 1.10.1 tables 3.6.1 tabulate 0.8.10 TBB 0.2 tblib 1.7.0 tenacity 8.0.1 terminado 0.13.1 testpath 0.6.0 text-unidecode 1.3 textdistance 4.2.1 threadpoolctl 2.2.0 three-merge 0.1.1 tifffile 2021.7.2 tinycss 0.4 tldextract 3.2.0 toml 0.10.2 tomli 2.0.1 tomlkit 0.11.1 toolz 0.11.2 tornado 6.1 tqdm 4.64.1 traitlets 5.1.1 Twisted 22.2.0 twisted-iocpsupport 1.0.2 typing_extensions 4.3.0 ujson 5.4.0 Unidecode 1.2.0 urllib3 1.26.11 w3lib 1.21.0 watchdog 2.1.6 wcwidth 0.2.5 webencodings 0.5.1 websocket-client 0.58.0 Werkzeug 2.0.3 wheel 0.37.1 widgetsnbextension 3.5.2 win-inet-pton 1.1.0 win-unicode-console 0.5 wincertstore 0.2 wrapt 1.14.1 xarray 0.20.1 xlrd 2.0.1 XlsxWriter 3.0.3 xlwings 0.27.15 yapf 0.31.0 zict 2.1.0 zipp 3.8.0 zope.interface 5.4.0

My main research direction is the preparation of monoclonal antibody, so I know little about computer program, and I am looking forward to your professional guidance.