ColabFold
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sokrypton
install dependencies error
Dependency issue in the install dependencies part of the code. Using use_templates=True, amber relax, and AlphaFold2_batch.ipynb Have others experienced this?
It fails on all: T4 GPU, L4 GPU, and A100 and the TPU v2.
All the best, N
ColabFold Output (for bugs)
`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)
4 frames
/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py 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\n\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# Download params (~1min)\npython -m colabfold.download\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.`
Can you share the command line?
just running the standard AlphafoldBatch Jupyter notebook on Google Colab: It runs:
`%%bash -s $use_amber $use_templates
set -e
USE_AMBER=$1 USE_TEMPLATES=$2
if [ ! -f COLABFOLD_READY ]; then pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold" pip install -q "jax[cuda11_cudnn805]>=0.3.8,<0.4" -f https://storage.googleapis.com/jax-releases/jax_releases.html touch COLABFOLD_READY fi`
I am trying to reproduce the issue but the batch notebook is working fine for me. Could you please post the full URL of the notebook you are using?
https://colab.research.google.com/github/konstin/ColabFold/blob/main/batch/AlphaFold2_batch.ipynb#scrollTo=iccGdbe_Pmt9
I must have an old link saved(^^). The current link works! Sorrrryyyy
works (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/batch/AlphaFold2_batch.ipynb#scrollTo=kOblAo-xetgx)