Shen-Lab / DeepAffinity

Protein-compound affinity prediction through unified RNN-CNN
GNU General Public License v3.0
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Can't create environment #14

Closed DBpackage closed 1 year ago

DBpackage commented 1 year ago

Hi, thank for your awesome works in DTA prediction, I really appreciate to your team!

I want to make the SPS sequence from my own protein data. I'm struggling to use the SSpro/ACCpro tool.

https://github.com/Shen-Lab/DeepAffinity/blob/master/DeepAffinity_Manual.pdf I refered this manual and I tried to create the conda environment for running the SSpro/ACCpro but I failed to create the environment.

I'm not major in the CS field. I'm sorry if my question is too basic 😭.

> Conda info active environment : base active env location : /home/miruware/anaconda3 shell level : 1 user config file : /home/miruware/.condarc populated config files : conda version : 4.10.3 conda-build version : 3.20.5 python version : 3.8.5.final.0 virtual packages : cuda=11.4=0 linux=5.15.0=0 glibc=2.31=0 unix=0=0 __archspec=1=x86_64 base environment : /home/miruware/anaconda3 (writable) conda av data dir : /home/miruware/anaconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/miruware/anaconda3/pkgs /home/miruware/.conda/pkgs envs directories : /home/miruware/anaconda3/envs /home/miruware/.conda/envs platform : linux-64 user-agent : conda/4.10.3 requests/2.24.0 CPython/3.8.5 Linux/5.15.0-60-generic ubuntu/20.04.2 glibc/2.31 UID:GID : 1000:1000 netrc file : None offline mode : False

> Conda list

Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py38_0 _libgcc_mutex 0.1 main absl-py 0.13.0 pypi_0 pypi alabaster 0.7.12 py_0 anaconda 2020.11 py38_0 anaconda-client 1.7.2 py38_0 anaconda-navigator 1.10.0 py38_0 anaconda-project 0.8.4 py_0 argh 0.26.2 py38_0 argon2-cffi 20.1.0 py38h7b6447c_1 asn1crypto 1.4.0 py_0 astroid 2.4.2 py38_0 astropy 4.0.2 py38h7b6447c_0 astunparse 1.6.3 pypi_0 pypi async_generator 1.10 py_0 atomicwrites 1.4.0 py_0 attrs 20.3.0 pyhd3eb1b0_0 autopep8 1.5.4 py_0 babel 2.8.1 pyhd3eb1b0_0 backcall 0.2.0 py_0 backports 1.0 py_2 backports.functools_lru_cache 1.6.1 py_0 backports.shutil_get_terminal_size 1.0.0 py38_2 backports.tempfile 1.0 py_1 backports.weakref 1.0.post1 py_1 beautifulsoup4 4.9.3 pyhb0f4dca_0 bitarray 1.6.1 py38h27cfd23_0 bkcharts 0.2 py38_0 blas 1.0 mkl bleach 3.2.1 py_0 blosc 1.20.1 hd408876_0 bokeh 2.2.3 py38_0 boto 2.49.0 py38_0 bottleneck 1.3.2 py38heb32a55_1 brotlipy 0.7.0 py38h7b6447c_1000 bzip2 1.0.8 h7b6447c_0 ca-certificates 2020.10.14 0 cachetools 4.2.2 pypi_0 pypi cairo 1.14.12 h8948797_3 certifi 2020.6.20 pyhd3eb1b0_3 cffi 1.14.3 py38he30daa8_0 chardet 3.0.4 py38_1003 click 7.1.2 py_0 cloudpickle 1.6.0 py_0 clyent 1.2.2 py38_1 colorama 0.4.4 py_0 conda 4.10.3 py38h06a4308_0 conda-build 3.20.5 py38_1 conda-env 2.6.0 1 conda-package-handling 1.7.2 py38h03888b9_0 conda-verify 3.4.2 py_1 contextlib2 0.6.0.post1 py_0 cryptography 3.1.1 py38h1ba5d50_0 cudatoolkit 11.0.221 h6bb024c_0 curl 7.71.1 hbc83047_1 cycler 0.10.0 py38_0 cython 0.29.21 py38he6710b0_0 cytoolz 0.11.0 py38h7b6447c_0 dask 2.30.0 py_0 dask-core 2.30.0 py_0 dbus 1.13.18 hb2f20db_0 decorator 4.4.2 py_0 defusedxml 0.6.0 py_0 diff-match-patch 20200713 py_0 distributed 2.30.1 py38h06a4308_0 docutils 0.16 py38_1 entrypoints 0.3 py38_0 et_xmlfile 1.0.1 py_1001 expat 2.2.10 he6710b0_2 fastcache 1.1.0 py38h7b6447c_0 filelock 3.0.12 py_0 flake8 3.8.4 py_0 flask 1.1.2 py_0 fontconfig 2.13.0 h9420a91_0 freetype 2.10.4 h5ab3b9f_0 fribidi 1.0.10 h7b6447c_0 fsspec 0.8.3 py_0 future 0.18.2 py38_1 gast 0.3.3 pypi_0 pypi get_terminal_size 1.0.0 haa9412d_0 gevent 20.9.0 py38h7b6447c_0 glib 2.66.1 h92f7085_0 glob2 0.7 py_0 gmp 6.1.2 h6c8ec71_1 gmpy2 2.0.8 py38hd5f6e3b_3 google-auth 1.35.0 pypi_0 pypi google-auth-oauthlib 0.4.5 pypi_0 pypi google-pasta 0.2.0 pypi_0 pypi graphite2 1.3.14 h23475e2_0 greenlet 0.4.17 py38h7b6447c_0 grpcio 1.39.0 pypi_0 pypi gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb31296c_0 h5py 2.10.0 py38h7918eee_0 harfbuzz 2.4.0 hca77d97_1 hdf5 1.10.4 hb1b8bf9_0 heapdict 1.0.1 py_0 html5lib 1.1 py_0 icu 58.2 he6710b0_3 idna 2.10 py_0 imageio 2.9.0 py_0 imagesize 1.2.0 py_0 importlib-metadata 2.0.0 py_1 importlib_metadata 2.0.0 1 iniconfig 1.1.1 py_0 intel-openmp 2020.2 254 intervaltree 3.1.0 py_0 ipykernel 5.3.4 py38h5ca1d4c_0 ipython 7.19.0 py38hb070fc8_0 ipython_genutils 0.2.0 py38_0 ipywidgets 7.5.1 py_1 isort 5.6.4 py_0 itsdangerous 1.1.0 py_0 jbig 2.1 hdba287a_0 jdcal 1.4.1 py_0 jedi 0.17.1 py38_0 jeepney 0.5.0 pyhd3eb1b0_0 jinja2 2.11.2 py_0 joblib 0.17.0 py_0 jpeg 9b h024ee3a_2 json5 0.9.5 py_0 jsonschema 3.2.0 py_2 jupyter 1.0.0 py38_7 jupyter_client 6.1.7 py_0 jupyter_console 6.2.0 py_0 jupyter_core 4.6.3 py38_0 jupyterlab 2.2.6 py_0 jupyterlab_pygments 0.1.2 py_0 jupyterlab_server 1.2.0 py_0 keras-preprocessing 1.1.2 pypi_0 pypi keyring 21.4.0 py38_1 kiwisolver 1.3.0 py38h2531618_0 krb5 1.18.2 h173b8e3_0 lazy-object-proxy 1.4.3 py38h7b6447c_0 lcms2 2.11 h396b838_0 ld_impl_linux-64 2.33.1 h53a641e_7 libarchive 3.4.2 h62408e4_0 libcurl 7.71.1 h20c2e04_1 libedit 3.1.20191231 h14c3975_1 libffi 3.3 he6710b0_2 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblief 0.10.1 he6710b0_0 libllvm10 10.0.1 hbcb73fb_5 libpng 1.6.37 hbc83047_0 libsodium 1.0.18 h7b6447c_0 libspatialindex 1.9.3 he6710b0_0 libssh2 1.9.0 h1ba5d50_1 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.1.0 h2733197_1 libtool 2.4.6 h7b6447c_1005 libuuid 1.0.3 h1bed415_2 libuv 1.40.0 h7b6447c_0 libxcb 1.14 h7b6447c_0 libxml2 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pyhd3eb1b0_1 oauthlib 3.1.1 pypi_0 pypi olefile 0.46 py_0 openpyxl 3.0.5 py_0 openssl 1.1.1h h7b6447c_0 opt-einsum 3.3.0 pypi_0 pypi packaging 20.4 py_0 pandas 1.1.3 py38he6710b0_0 pandoc 2.11 hb0f4dca_0 pandocfilters 1.4.3 py38h06a4308_1 pango 1.45.3 hd140c19_0 parso 0.7.0 py_0 partd 1.1.0 py_0 patchelf 0.12 he6710b0_0 path 15.0.0 py38_0 path.py 12.5.0 0 pathlib2 2.3.5 py38_0 pathtools 0.1.2 py_1 patsy 0.5.1 py38_0 pcre 8.44 he6710b0_0 pep8 1.7.1 py38_0 pexpect 4.8.0 py38_0 pickleshare 0.7.5 py38_1000 pillow 8.0.1 py38he98fc37_0 pip 20.2.4 py38h06a4308_0 pixman 0.40.0 h7b6447c_0 pkginfo 1.6.1 py38h06a4308_0 pluggy 0.13.1 py38_0 ply 3.11 py38_0 prometheus_client 0.8.0 py_0 prompt-toolkit 3.0.8 py_0 prompt_toolkit 3.0.8 0 protobuf 3.17.3 pypi_0 pypi psutil 5.7.2 py38h7b6447c_0 ptyprocess 0.6.0 py38_0 py 1.9.0 py_0 py-lief 0.10.1 py38h403a769_0 pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pycodestyle 2.6.0 py_0 pycosat 0.6.3 py38h7b6447c_1 pycparser 2.20 py_2 pycurl 7.43.0.6 py38h1ba5d50_0 pydocstyle 5.1.1 py_0 pyflakes 2.2.0 py_0 pygments 2.7.2 pyhd3eb1b0_0 pylint 2.6.0 py38_0 pyodbc 4.0.30 py38he6710b0_0 pyopenssl 19.1.0 py_1 pyparsing 2.4.7 py_0 pyqt 5.9.2 py38h05f1152_4 pyrsistent 0.17.3 py38h7b6447c_0 pysocks 1.7.1 py38_0 pytables 3.6.1 py38h9fd0a39_0 pytest 6.1.1 py38_0 python 3.8.5 h7579374_1 python-dateutil 2.8.1 py_0 python-jsonrpc-server 0.4.0 py_0 python-language-server 0.35.1 py_0 python-libarchive-c 2.9 py_0 pytorch 1.7.1 py3.8_cuda11.0.221_cudnn8.0.5_0 pytorch pytz 2020.1 py_0 pywavelets 1.1.1 py38h7b6447c_2 pyxdg 0.27 pyhd3eb1b0_0 pyyaml 5.3.1 py38h7b6447c_1 pyzmq 19.0.2 py38he6710b0_1 qdarkstyle 2.8.1 py_0 qt 5.9.7 h5867ecd_1 qtawesome 1.0.1 py_0 qtconsole 4.7.7 py_0 qtpy 1.9.0 py_0 readline 8.0 h7b6447c_0 regex 2020.10.15 py38h7b6447c_0 requests 2.24.0 py_0 requests-oauthlib 1.3.0 pypi_0 pypi ripgrep 12.1.1 0 rope 0.18.0 py_0 rsa 4.7.2 pypi_0 pypi rtree 0.9.4 py38_1 ruamel_yaml 0.15.87 py38h7b6447c_1 scikit-image 0.17.2 py38hdf5156a_0 scikit-learn 0.23.2 py38h0573a6f_0 scipy 1.4.1 pypi_0 pypi seaborn 0.11.0 py_0 secretstorage 3.1.2 py38_0 send2trash 1.5.0 py38_0 setuptools 50.3.1 py38h06a4308_1 simplegeneric 0.8.1 py38_2 singledispatch 3.4.0.3 py_1001 sip 4.19.13 py38he6710b0_0 six 1.15.0 py38h06a4308_0 snowballstemmer 2.0.0 py_0 sortedcollections 1.2.1 py_0 sortedcontainers 2.2.2 py_0 soupsieve 2.0.1 py_0 sphinx 3.2.1 py_0 sphinxcontrib 1.0 py38_1 sphinxcontrib-applehelp 1.0.2 py_0 sphinxcontrib-devhelp 1.0.2 py_0 sphinxcontrib-htmlhelp 1.0.3 py_0 sphinxcontrib-jsmath 1.0.1 py_0 sphinxcontrib-qthelp 1.0.3 py_0 sphinxcontrib-serializinghtml 1.1.4 py_0 sphinxcontrib-websupport 1.2.4 py_0 spyder 4.1.5 py38_0 spyder-kernels 1.9.4 py38_0 sqlalchemy 1.3.20 py38h7b6447c_0 sqlite 3.33.0 h62c20be_0 statsmodels 0.12.0 py38h7b6447c_0 sympy 1.6.2 py38h06a4308_1 tbb 2020.3 hfd86e86_0 tblib 1.7.0 py_0 tensorboard 2.2.2 pypi_0 pypi tensorboard-plugin-wit 1.8.0 pypi_0 pypi tensorflow-estimator 2.2.0 pypi_0 pypi tensorflow-gpu 2.2.0 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi terminado 0.9.1 py38_0 testpath 0.4.4 py_0 threadpoolctl 2.1.0 pyh5ca1d4c_0 tifffile 2020.10.1 py38hdd07704_2 tk 8.6.10 hbc83047_0 toml 0.10.1 py_0 toolz 0.11.1 py_0 torchaudio 0.7.2 py38 pytorch torchvision 0.8.2 py38_cu110 pytorch tornado 6.0.4 py38h7b6447c_1 tqdm 4.50.2 py_0 traitlets 5.0.5 py_0 typing_extensions 3.7.4.3 py_0 ujson 4.0.1 py38he6710b0_0 unicodecsv 0.14.1 py38_0 unixodbc 2.3.9 h7b6447c_0 urllib3 1.25.11 py_0 watchdog 0.10.3 py38_0 wcwidth 0.2.5 py_0 webencodings 0.5.1 py38_1 werkzeug 1.0.1 py_0 wheel 0.35.1 py_0 widgetsnbextension 3.5.1 py38_0 wrapt 1.11.2 py38h7b6447c_0 wurlitzer 2.0.1 py38_0 xlrd 1.2.0 py_0 xlsxwriter 1.3.7 py_0 xlwt 1.3.0 py38_0 xmltodict 0.12.0 py_0 xz 5.2.5 h7b6447c_0 yaml 0.2.5 h7b6447c_0 yapf 0.30.0 py_0 zeromq 4.3.3 he6710b0_3 zict 2.0.0 py_0 zipp 3.4.0 pyhd3eb1b0_0 zlib 1.2.11 h7b6447c_3 zope 1.0 py38_1 zope.event 4.5.0 py38_0 zope.interface 5.1.2 py38h7b6447c_0 zstd 1.4.5 h9ceee32_0

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