error whole running alphafold google colab

[Dhire123]

I came across following error while running alphafold google colab. could you please help me resolve the problem.

WARNING: Skipping tensorflow as it is not installed.
WARNING: Skipping keras as it is not installed.
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Reading package lists...
Building dependency tree...
Reading state information...
hmmer is already the newest version (3.3.2+dfsg-1).
0 upgraded, 0 newly installed, 0 to remove and 35 not upgraded.
Collecting py3dmol
Using cached py3Dmol-2.0.4-py2.py3-none-any.whl.metadata (2.1 kB)
Using cached py3Dmol-2.0.4-py2.py3-none-any.whl (12 kB)
Installing collected packages: py3dmol
Successfully installed py3dmol-2.0.4
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
PREFIX=/opt/conda
Unpacking payload ...

Installing base environment...

Downloading and Extracting Packages:

Downloading and Extracting Packages:

Preparing transaction: done
Executing transaction: done
installation finished.
WARNING:
You currently have a PYTHONPATH environment variable set. This may cause
unexpected behavior when running the Python interpreter in Miniconda3.
For best results, please verify that your PYTHONPATH only points to
directories of packages that are compatible with the Python interpreter
in Miniconda3: /opt/conda
env: PATH=/opt/conda/bin:/opt/conda/bin:/opt/conda/bin:/opt/conda/bin:/opt/conda/bin:/opt/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-sdk/bin
Channels:

• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): ...working... done
  Solving environment: ...working... warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
  failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• package conda-23.5.2-py310h06a4308_0 requires python >=3.10,<3.11.0a0, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ conda 23.5.2 is installable with the potential options
│ ├─ conda 23.5.2 would require
│ │ └─ python >=3.10,<3.11.0a0 , which can be installed;
│ ├─ conda 23.5.2 would require
│ │ └─ python >=3.11,<3.12.0a0 , which can be installed;
│ ├─ conda 23.5.2 would require
│ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
│ └─ conda 23.5.2 would require
│ └─ python >=3.9,<3.10.0a0 , which can be installed;
└─ pin-1 is not installable because it requires
└─ python 3.12.* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:

• python 3.12.* (labeled as 'pin-1')

---

CalledProcessError Traceback (most recent call last)
in <cell line: 22>()
40 PATH=get_ipython().run_line_magic('env', 'PATH')
41 get_ipython().run_line_magic('env', 'PATH=/opt/conda/bin:{PATH}')
---> 42 get_ipython().run_line_magic('shell', 'conda install -qy conda==23.5.2 && conda install -qy -c conda-forge python=3.10 openmm=7.7.0 pdbfixer')
43 pbar.update(80)
44

2 frames
/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
2416 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2417 with self.builtin_trap:
-> 2418 result = fn(*args, **kwargs)
2419 return result
2420

/usr/local/lib/python3.10/dist-packages/google/colab/_system_commands.py in _shell_line_magic(line)
65 """
66 result = _run_command(line, clear_streamed_output=False)
---> 67 result.check_returncode()
68 return result
69

/usr/local/lib/python3.10/dist-packages/google/colab/_system_commands.py in check_returncode(self)
135 def check_returncode(self):
136 if self.returncode:
--> 137 raise subprocess.CalledProcessError(
138 returncode=self.returncode, cmd=self.args, output=self.output
139 )

CalledProcessError: Command 'conda install -qy conda==23.5.2 && conda install -qy -c conda-forge python=3.10 openmm=7.7.0 pdbfixer' returned non-zero exit status 1.

[farshadf]

I am experiencing the same issue. Removing version constrain on conda and changing the python version to 3.12 helped me to go through this step. However, I am experiencing the version issue when trying to install the requirements.txt at the next step. This is the issue I receive on the next step:

8%
 8/100 [elapsed: 00:16 remaining: 00:22]

Cloning into 'alphafold'...
remote: Enumerating objects: 956, done.
remote: Counting objects: 100% (6/6), done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 956 (delta 0), reused 3 (delta 0), pack-reused 950
Receiving objects: 100% (956/956), 16.27 MiB | 20.07 MiB/s, done.
Resolving deltas: 100% (581/581), done.
Collecting absl-py==1.0.0 (from -r ./alphafold/requirements.txt (line 1))
  Downloading absl_py-1.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting biopython==1.79 (from -r ./alphafold/requirements.txt (line 2))
  Downloading biopython-1.79.tar.gz (16.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.7/16.7 MB 81.5 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting chex==0.0.7 (from -r ./alphafold/requirements.txt (line 3))
  Downloading chex-0.0.7-py3-none-any.whl.metadata (14 kB)
Collecting dm-haiku==0.0.10 (from -r ./alphafold/requirements.txt (line 4))
  Downloading dm_haiku-0.0.10-py3-none-any.whl.metadata (18 kB)
Collecting dm-tree==0.1.8 (from -r ./alphafold/requirements.txt (line 5))
  Downloading dm_tree-0.1.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.9 kB)
Collecting docker==5.0.0 (from -r ./alphafold/requirements.txt (line 6))
  Downloading docker-5.0.0-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting immutabledict==2.0.0 (from -r ./alphafold/requirements.txt (line 7))
  Downloading immutabledict-2.0.0-py3-none-any.whl.metadata (2.7 kB)
Collecting jax==0.4.14 (from -r ./alphafold/requirements.txt (line 8))
  Downloading jax-0.4.14.tar.gz (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 64.7 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting ml-collections==0.1.0 (from -r ./alphafold/requirements.txt (line 9))
  Downloading ml_collections-0.1.0-py3-none-any.whl.metadata (18 kB)
Collecting numpy==1.24.3 (from -r ./alphafold/requirements.txt (line 10))
  Downloading numpy-1.24.3.tar.gz (10.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.9/10.9 MB 102.5 MB/s eta 0:00:00
  Installing build dependencies ... done
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  Getting requirements to build wheel ... error
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

---------------------------------------------------------------------------

CalledProcessError                        Traceback (most recent call last)

[<ipython-input-3-b9439fbeec6b>](https://localhost:8080/#) in <cell line: 11>()
     16       pbar.update(8)
     17       # Install the required versions of all dependencies.
---> 18       get_ipython().run_line_magic('shell', 'pip3 install -r ./alphafold/requirements.txt')
     19       # Run setup.py to install only AlphaFold.
     20       get_ipython().run_line_magic('shell', 'pip3 install --no-dependencies ./alphafold')

2 frames

[/usr/local/lib/python3.10/dist-packages/google/colab/_system_commands.py](https://localhost:8080/#) in check_returncode(self)
    135   def check_returncode(self):
    136     if self.returncode:
--> 137       raise subprocess.CalledProcessError(
    138           returncode=self.returncode, cmd=self.args, output=self.output
    139       )

CalledProcessError: Command 'pip3 install -r ./alphafold/requirements.txt' returned non-zero exit status 1.

Any help will be appreciated.

[farshadf]

@Dhire123 it seems a solution is suggested already in another issue #903