CalledProcessError Cannot install jax Run crashes at install dependencies

Expected Behavior

I was able to run Alphafold2 no issues Oct 28. For the past week I cannot get it to run or fix the code based on gemini recommendations.

Current Behavior

Run stops at the install dependencies section as an error comes up.

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

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...

4 frames
in shebang(self, line, cell)

/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\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.

Context

I have tried to restart but issue is recurring for multiple days. I'm only beginner at this so sorry if error context is unclear I can answer questions if needed.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used
• If you run it on a local system. Please add the server specifications
• Operating system and version:
  I just run the basic version of AlphaFold2 online on colabfold. I don't change any variables or anything and I run on the free version usually with GPU. I'm on a laptop with Windows 11.

The failing entry point is the Colab notebook's bash install-dependencies cell, especially the pip installation commands for ColabFold and JAX. Start by reproducing after a Colab factory reset and inspect the complete pip output; done means dependency setup completes and the notebook proceeds.