huhlim / alphafold-multistate Goto Github PK

query_align = next(iter(sequence_dict.values()))
StopIteration

installing colabfold...
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installing conda...
warning  libmamba [python-3.10.14-hd12c33a_0_cpython] The following files were already present in the environment:
    - bin/python
warning  libmamba [charset-normalizer-3.3.2-pyhd8ed1ab_0] The following files were already present in the environment:
    - bin/normalizer
warning  libmamba [wheel-0.43.0-pyhd8ed1ab_0] The following files were already present in the environment:
    - bin/wheel
warning  libmamba [pip-24.0-pyhd8ed1ab_0] The following files were already present in the environment:
    - bin/pip
    - bin/pip3
warning  libmamba [tqdm-4.66.2-pyhd8ed1ab_0] The following files were already present in the environment:
    - bin/tqdm
Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba.
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
[<ipython-input-2-c7ae885addc1>](https://localhost:8080/#) in <cell line: 1>()
----> 1 get_ipython().run_cell_magic('bash', '-s $use_amber $use_templates $python_version', '\nset -e\n\nUSE_AMBER=$1\nUSE_TEMPLATES=$2\nPYTHON_VERSION=$3\n\nif [ ! -f COLABFOLD_READY ]; then\n  echo "installing colabfold..."\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  ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n  ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n  touch COLABFOLD_READY\nfi\n\n# setup conda\nif [ ${USE_AMBER} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then\n  if [ ! -f CONDA_READY ]; then\n    echo "installing conda..."\n    wget -qnc [https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\n](https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh/n)    bash Mambaforge-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n    rm Mambaforge-Linux-x86_64.sh\n    mamba config --set auto_update_conda false\n    touch CONDA_READY\n  fi\nfi\n# setup template search\nif [ ${USE_TEMPLATES} == "True" ] && [ ! -f HH_READY ]; then\n  conda install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 python="${PYTHON_VERSION}" gdown 2>&1 1>/dev/null\n  touch HH_READY\nfi\n\nif [ ! -e colabfold_runner.py...

4 frames
[/usr/local/lib/python3.10/dist-packages/google/colab/_shell.py](https://localhost:8080/#) in run_cell_magic(self, magic_name, line, cell)
    332     if line and not cell:
    333       cell = ' '
--> 334     return super().run_cell_magic(magic_name, line, cell)
    335 
    336 

[/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py](https://localhost:8080/#) in run_cell_magic(self, magic_name, line, cell)
   2471             with self.builtin_trap:
   2472                 args = (magic_arg_s, cell)
-> 2473                 result = fn(*args, **kwargs)
   2474             return result
   2475 

[/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py](https://localhost:8080/#) in named_script_magic(line, cell)
    140             else:
    141                 line = script
--> 142             return self.shebang(line, cell)
    143 
    144         # write a basic docstring:

<decorator-gen-103> in shebang(self, line, cell)

[/usr/local/lib/python3.10/dist-packages/IPython/core/magic.py](https://localhost:8080/#) in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

[/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py](https://localhost:8080/#) in shebang(self, line, cell)
    243             sys.stderr.flush()
    244         if args.raise_error and p.returncode!=0:
--> 245             raise CalledProcessError(p.returncode, cell, output=out, stderr=err)
    246 
    247     def _run_script(self, p, cell, to_close):

CalledProcessError: Command 'b'\nset -e\n\nUSE_AMBER=$1\nUSE_TEMPLATES=$2\nPYTHON_VERSION=$3\n\nif [ ! -f COLABFOLD_READY ]; then\n  echo "installing colabfold..."\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  ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n  ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n  touch COLABFOLD_READY\nfi\n\n# setup conda\nif [ ${USE_AMBER} == "True" ] || [ ${USE_TEMPLATES} == "True" ]; then\n  if [ ! -f CONDA_READY ]; then\n    echo "installing conda..."\n    wget -qnc [https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\n](https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh/n)    bash Mambaforge-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n    rm Mambaforge-Linux-x86_64.sh\n    mamba config --set auto_update_conda false\n    touch CONDA_READY\n  fi\nfi\n# setup template search\nif [ ${USE_TEMPLATES} == "True" ] && [ ! -f HH_READY ]; then\n  conda install -y -q -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 python="${PYTHON_VERSION}" gdown 2>&1 1>/dev/null\n  touch HH_READY\nfi\n\nif [ ! -e colabfold_runner.py ]; then\n  wget -q [https://raw.githubusercontent.com/huhlim/alphafold-multistate/main/structure_prediction/colabfold_runner.py\nfi\n](https://raw.githubusercontent.com/huhlim/alphafold-multistate/main/structure_prediction/colabfold_runner.py/nfi/n)'' returned non-zero exit status 1.