Error in ' install dependencies"

[christinapapa]

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) in <cell line: 1>() ----> 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 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 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 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 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 ?

[supekshala]

It appears you're encountering an issue with installing dependencies for ColabFold, specifically related to the jax package. This error suggests there are conflicting dependencies between different versions of jax that are being requested. Here are some steps you can try to resolve this issue:

1. Update ColabFold: Make sure you're using the latest version of ColabFold. The developers frequently update the package to fix compatibility issues.

2. Clear the Colab runtime: If you're using Google Colab, try clearing the runtime and starting fresh. Go to "Runtime" in the menu and select "Restart runtime".

3. Specify a compatible jax version: Try specifying a specific version of jax that is known to work with ColabFold. You can do this by adding the following line before running the installation:

!pip install jax[cuda11_cudnn805]==0.3.25

4. Update CUDA and cuDNN: Ensure that your CUDA and cuDNN versions are compatible with the jax versions being requested. You might need to update these on your system.

5. Use a different environment: If you're running this locally, consider creating a new virtual environment to avoid conflicts with existing packages.

6. Try a different MSA mode: If the issue persists, you could try changing the MSA mode from MMseqs2(UniRef+Environmental) to another option, such as MMseqs2(UniRef only) or even HHblits if available.

7. Check for system compatibility: Ensure that your system meets all the requirements for running ColabFold, including having a compatible GPU if you're using GPU acceleration.

Remember, ColabFold is an actively developed tool that combines multiple complex components (AlphaFold2, MMseqs2, etc.), so occasional compatibility issues are not uncommon[3][6]. The developers regularly work on improving its stability and compatibility across different environments.