google-deepmind / google-deepmind/alphafold
Error in ' install dependencies"
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Description
hello ! I've got a problem with ColabFold: AlphaFold2 using MMseqs2 , when I use the sequence of a-synuclein (MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTK
EQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDP
DNEAYEMPSEEGYQDYEPEA ) ( I tried it also with other sequencies), with amber , no pdb70 template mode, msa_mode: MMseqs2(UniRef+Environmental), pair_mode: unpaired+paired, model_type: AlphaFold2-ptm, in section install dependencies I get this
```
ERROR: Cannot install jax[cuda11-cudnn805]==0.3.10, jax[cuda11-cudnn805]==0.3.11, jax[cuda11-cudnn805]==0.3.12, jax[cuda11-cudnn805]==0.3.13, jax[cuda11-cudnn805]==0.3.14, jax[cuda11-cudnn805]==0.3.15, jax[cuda11-cudnn805]==0.3.16, jax[cuda11-cudnn805]==0.3.17, jax[cuda11-cudnn805]==0.3.18, jax[cuda11-cudnn805]==0.3.19, jax[cuda11-cudnn805]==0.3.20, jax[cuda11-cudnn805]==0.3.21, jax[cuda11-cudnn805]==0.3.22, jax[cuda11-cudnn805]==0.3.23, jax[cuda11-cudnn805]==0.3.24, jax[cuda11-cudnn805]==0.3.25, jax[cuda11-cudnn805]==0.3.8 and jax[cuda11-cudnn805]==0.3.9 because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
[](https://localhost:8080/#) in ()
----> 1 get_ipython().run_cell_magic('bash', '-s $use_amber $use_templates', '\nset -e\n\nUSE_AMBER=$1\nUSE_TEMPLATES=$2\n\nif [ ! -f COLABFOLD_READY ]; then\n # install dependencies\n # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours\n pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"\n # high risk high gain\n pip install -q "jax[cuda11_cudnn805]>=0.3.8,<0.4" -f [https://storage.googleapis.com/jax-releases/jax_releases.html\n](https://storage.googleapis.com/jax-releases/jax_releases.html/n) touch COLABFOLD_READY\nfi\n\n# setup conda\nif [ ${USE_AMBER} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then\n if [ ! -f CONDA_READY ]; then\n wget -qnc [https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh/n) bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n rm Miniconda3-latest-Linux-x86_64.sh\n touch CONDA_READY\n fi\nfi\n# setup template search\nif [ ${USE_TEMPLATES} == "True" ] && [ ! -f HH_READY ]; then\n conda install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 python=3.7 2>&1 1>/dev/null\n touch HH_READY\nfi\n# setup openmm for amber refinement\nif [ ${USE_AMBER} == "True" ] && [ ! -f AMBER_READY ]; then\n conda install -y -q -c conda-forge openmm=7.5.1 python=3.7 pdbfixer 2>&1 1>/dev/null\n touch AMBER_READ...
CalledProcessError: Command 'b'\nset -e\n\nUSE_AMBER=$1\nUSE_TEMPLATES=$2\n\nif [ ! -f COLABFOLD_READY ]; then\n # install dependencies\n # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours\n pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"\n # high risk high gain\n pip install -q "jax[cuda11_cudnn805]>=0.3.8,<0.4" -f [https://storage.googleapis.com/jax-releases/jax_releases.html\n](https://storage.googleapis.com/jax-releases/jax_releases.html/n) touch COLABFOLD_READY\nfi\n\n# setup conda\nif [ ${USE_AMBER} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then\n if [ ! -f CONDA_READY ]; then\n wget -qnc [https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh/n) bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n rm Miniconda3-latest-Linux-x86_64.sh\n touch CONDA_READY\n fi\nfi\n# setup template search\nif [ ${USE_TEMPLATES} == "True" ] && [ ! -f HH_READY ]; then\n conda install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 python=3.7 2>&1 1>/dev/null\n touch HH_READY\nfi\n# setup openmm for amber refinement\nif [ ${USE_AMBER} == "True" ] && [ ! -f AMBER_READY ]; then\n conda install -y -q -c conda-forge openmm=7.5.1 python=3.7 pdbfixer 2>&1 1>/dev/null\n touch AMBER_READY\nfi\n'' returned non-zero exit status 1.
```
Do you maybe know what's wrong ?
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