+ set -e
+ pip install --no-warn-conflicts 'colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72'
Collecting colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Cloning https://github.com/sokrypton/ColabFold (to revision 29395e7dee2c2895eaf585ef6b6cde932fd95e72) to /tmp/pip-install-_qen4b6y/colabfold_c0dd8ad74f034fe8be2cd75edd520a77
  Running command git clone --filter=blob:none --quiet https://github.com/sokrypton/ColabFold /tmp/pip-install-_qen4b6y/colabfold_c0dd8ad74f034fe8be2cd75edd520a77
  Running command git rev-parse -q --verify 'sha^29395e7dee2c2895eaf585ef6b6cde932fd95e72'
  Running command git fetch -q https://github.com/sokrypton/ColabFold 29395e7dee2c2895eaf585ef6b6cde932fd95e72
  Running command git checkout -q 29395e7dee2c2895eaf585ef6b6cde932fd95e72
  Resolved https://github.com/sokrypton/ColabFold to commit 29395e7dee2c2895eaf585ef6b6cde932fd95e72
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: absl-py<2.0.0,>=1.0.0 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.4.0)
Collecting appdirs<2.0.0,>=1.4.4 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting dm-haiku<0.0.10,>=0.0.9 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading dm_haiku-0.0.9-py3-none-any.whl.metadata (18 kB)
Collecting importlib-metadata<5.0.0,>=4.8.2 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading importlib_metadata-4.13.0-py3-none-any.whl.metadata (4.9 kB)
Requirement already satisfied: matplotlib<4.0.0,>=3.2.2 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.7.1)
Requirement already satisfied: numpy<2.0.0,>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.26.4)
Collecting pandas<2.0.0,>=1.3.4 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting py3Dmol<3.0.0,>=2.0.1 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading py3Dmol-2.4.0-py2.py3-none-any.whl.metadata (1.9 kB)
Requirement already satisfied: requests<3.0.0,>=2.26.0 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.32.3)
Collecting tensorflow-cpu<3.0.0,>=2.11.0 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading tensorflow_cpu-2.18.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB)
Requirement already satisfied: tqdm<5.0.0,>=4.62.2 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.66.5)
Collecting alphafold-colabfold==v2.3.5 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading alphafold_colabfold-2.3.5-py3-none-any.whl.metadata (1.3 kB)
Collecting biopython (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Requirement already satisfied: chex in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.1.87)
Requirement already satisfied: dm-tree in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.1.8)
Collecting docker (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading docker-7.1.0-py3-none-any.whl.metadata (3.8 kB)
Requirement already satisfied: immutabledict in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.2.0)
Requirement already satisfied: jax in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.4.33)
Collecting ml-collections (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading ml_collections-0.1.1.tar.gz (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.9/77.9 kB 7.6 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.13.1)
Collecting jmp>=0.0.2 (from dm-haiku<0.0.10,>=0.0.9->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading jmp-0.0.4-py3-none-any.whl.metadata (8.9 kB)
Requirement already satisfied: tabulate>=0.8.9 in /usr/local/lib/python3.10/dist-packages (from dm-haiku<0.0.10,>=0.0.9->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.9.0)
Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.10/dist-packages (from importlib-metadata<5.0.0,>=4.8.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.20.2)
Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.3.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.54.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.4.7)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (24.1)
Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (10.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.2.0)
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Requirement already satisfied: grpcio<2.0,>=1.24.3 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.64.1)
Collecting tensorboard<2.19,>=2.18 (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading tensorboard-2.18.0-py3-none-any.whl.metadata (1.6 kB)
Collecting keras>=3.5.0 (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading keras-3.6.0-py3-none-any.whl.metadata (5.8 kB)
Requirement already satisfied: h5py>=3.11.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.11.0)
Requirement already satisfied: ml-dtypes<0.5.0,>=0.4.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.4.1)
Requirement already satisfied: tensorflow-io-gcs-filesystem>=0.23.1 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.37.1)
Requirement already satisfied: wheel<1.0,>=0.23.0 in /usr/local/lib/python3.10/dist-packages (from astunparse>=1.6.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.44.0)
Requirement already satisfied: rich in /usr/local/lib/python3.10/dist-packages (from keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (13.9.3)
Requirement already satisfied: namex in /usr/local/lib/python3.10/dist-packages (from keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.0.8)
Requirement already satisfied: optree in /usr/local/lib/python3.10/dist-packages (from keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.13.0)
Requirement already satisfied: markdown>=2.6.8 in /usr/local/lib/python3.10/dist-packages (from tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.7)
Requirement already satisfied: tensorboard-data-server<0.8.0,>=0.7.0 in /usr/local/lib/python3.10/dist-packages (from tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.7.2)
Requirement already satisfied: werkzeug>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.0.6)
Requirement already satisfied: jaxlib>=0.4.27 in /usr/local/lib/python3.10/dist-packages (from chex->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.4.33)
Requirement already satisfied: toolz>=0.9.0 in /usr/local/lib/python3.10/dist-packages (from chex->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.12.1)
Requirement already satisfied: PyYAML in /usr/local/lib/python3.10/dist-packages (from ml-collections->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (6.0.2)
Collecting contextlib2 (from ml-collections->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
  Downloading contextlib2-21.6.0-py2.py3-none-any.whl.metadata (4.1 kB)
Requirement already satisfied: MarkupSafe>=2.1.1 in /usr/local/lib/python3.10/dist-packages (from werkzeug>=1.0.1->tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.0.2)
Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.10/dist-packages (from rich->keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.0.0)
Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/dist-packages (from rich->keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.18.0)
Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.10/dist-packages (from markdown-it-py>=2.2.0->rich->keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.1.2)
Downloading alphafold_colabfold-2.3.5-py3-none-any.whl (242 kB)
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Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Downloading dm_haiku-0.0.9-py3-none-any.whl (352 kB)
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Downloading importlib_metadata-4.13.0-py3-none-any.whl (23 kB)
Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
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Downloading py3Dmol-2.4.0-py2.py3-none-any.whl (7.0 kB)
Downloading tensorflow_cpu-2.18.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (230.0 MB)
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Downloading jmp-0.0.4-py3-none-any.whl (18 kB)
Downloading keras-3.6.0-py3-none-any.whl (1.2 MB)
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Downloading tensorboard-2.18.0-py3-none-any.whl (5.5 MB)
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Downloading biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
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Downloading docker-7.1.0-py3-none-any.whl (147 kB)
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Downloading contextlib2-21.6.0-py2.py3-none-any.whl (13 kB)
Building wheels for collected packages: colabfold, ml-collections
  Building wheel for colabfold (pyproject.toml): started
  Building wheel for colabfold (pyproject.toml): finished with status 'done'
  Created wheel for colabfold: filename=colabfold-1.5.3-py3-none-any.whl size=61553 sha256=6d7228b96fbbe94d6f7afdb014227d4cb84c1ff14690d07f9eb67724122c2d37
  Stored in directory: /root/.cache/pip/wheels/0a/84/5a/d55512132cfd5a14ace505b83af68d378992924dd8ea760c72
  Building wheel for ml-collections (setup.py): started
  Building wheel for ml-collections (setup.py): finished with status 'done'
  Created wheel for ml-collections: filename=ml_collections-0.1.1-py3-none-any.whl size=94508 sha256=96f9c8d5ef8bbcffb1eb73289a1ad46bb57fe46029d7f2a9407b79d2ac7e0aaf
  Stored in directory: /root/.cache/pip/wheels/7b/89/c9/a9b87790789e94aadcfc393c283e3ecd5ab916aed0a31be8fe
Successfully built colabfold ml-collections
Installing collected packages: py3Dmol, appdirs, jmp, importlib-metadata, contextlib2, biopython, tensorboard, pandas, ml-collections, docker, dm-haiku, keras, tensorflow-cpu, colabfold, alphafold-colabfold
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib_metadata 8.5.0
    Uninstalling importlib_metadata-8.5.0:
      Successfully uninstalled importlib_metadata-8.5.0
  Attempting uninstall: tensorboard
    Found existing installation: tensorboard 2.17.0
    Uninstalling tensorboard-2.17.0:
      Successfully uninstalled tensorboard-2.17.0
  Attempting uninstall: pandas
    Found existing installation: pandas 2.2.2
    Uninstalling pandas-2.2.2:
      Successfully uninstalled pandas-2.2.2
  Attempting uninstall: keras
    Found existing installation: keras 3.4.1
    Uninstalling keras-3.4.1:
      Successfully uninstalled keras-3.4.1
Successfully installed alphafold-colabfold-2.3.5 appdirs-1.4.4 biopython-1.84 colabfold-1.5.3 contextlib2-21.6.0 dm-haiku-0.0.9 docker-7.1.0 importlib-metadata-4.13.0 jmp-0.0.4 keras-3.6.0 ml-collections-0.1.1 pandas-1.5.3 py3Dmol-2.4.0 tensorboard-2.18.0 tensorflow-cpu-2.18.0
+ pip install --upgrade dm-haiku
Requirement already satisfied: dm-haiku in /usr/local/lib/python3.10/dist-packages (0.0.9)
Collecting dm-haiku
  Downloading dm_haiku-0.0.13-py3-none-any.whl.metadata (19 kB)
Requirement already satisfied: absl-py>=0.7.1 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (1.4.0)
Requirement already satisfied: jmp>=0.0.2 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (0.0.4)
Requirement already satisfied: numpy>=1.18.0 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (1.26.4)
Requirement already satisfied: tabulate>=0.8.9 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (0.9.0)
Downloading dm_haiku-0.0.13-py3-none-any.whl (373 kB)
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Installing collected packages: dm-haiku
  Attempting uninstall: dm-haiku
    Found existing installation: dm-haiku 0.0.9
    Uninstalling dm-haiku-0.0.9:
      Successfully uninstalled dm-haiku-0.0.9
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
colabfold 1.5.3 requires dm-haiku<0.0.10,>=0.0.9, but you have dm-haiku 0.0.13 which is incompatible.
Successfully installed dm-haiku-0.0.13
+ sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' /usr/local/lib/python3.10/dist-packages/alphafold/model/modules.py
+ pip install biopython==1.81
Collecting biopython==1.81
  Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython==1.81) (1.26.4)
Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
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Installing collected packages: biopython
  Attempting uninstall: biopython
    Found existing installation: biopython 1.84
    Uninstalling biopython-1.84:
      Successfully uninstalled biopython-1.84
Successfully installed biopython-1.81
+ touch COLABFOLD_READY
+ set -e
+ wget -qnc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local
+ rm Miniconda3-latest-Linux-x86_64.sh
+ touch CONDA_READY
+ set -e
+ conda install -y -q -c conda-forge openmm=7.7.0 python=3.10 pdbfixer
+ ln -s /usr/local/lib/python3.10/site-packages/simtk .
+ ln -s /usr/local/lib/python3.10/site-packages/openmm .
+ ln -s /usr/local/lib/python3.10/site-packages/pdbfixer .
+ touch AMBER_READY