Google collab error

[irinasspider]

I am trying to run OmegaFold on Google collab, but with the test sequence I always get this error: ModuleNotFoundError: No module named 'Bio.Data.SCOPData'

CalledProcessError Traceback (most recent call last) in <cell line: 42>() 40 out.write(f">{ID}\n{sequence}\n") 41 ---> 42 get_ipython().run_line_magic('shell', 'python OmegaFold/main.py --offset_rope={offset_rope} --device={device} --subbatch_size={subbatch_size} --num_cycle={num_cycle} {ID}.fasta .') 43 44 def renum_pdb_str(pdb_str, Ls=None, renum=True, offset=1):

2 frames /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 'python OmegaFold/main.py --offset_rope=False --device=cuda --subbatch_size=500 --num_cycle=4 test_a5e17.fasta .' returned non-zero exit status 1.

[hhuang-code]

I am trying to run OmegaFold on Google collab, but with the test sequence I always get this error:

ModuleNotFoundError: No module named 'Bio.Data.SCOPData' CalledProcessError Traceback (most recent call last) in <cell line: 42>() 40 out.write(f">{ID}\n{sequence}\n") 41 ---> 42 get_ipython().run_line_magic('shell', 'python OmegaFold/main.py --offset_rope={offset_rope} --device={device} --subbatch_size={subbatch_size} --num_cycle={num_cycle} {ID}.fasta .') 43 44 def renum_pdb_str(pdb_str, Ls=None, renum=True, offset=1):

2 frames /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 'python OmegaFold/main.py --offset_rope=False --device=cuda --subbatch_size=500 --num_cycle=4 test_a5e17.fasta .' returned non-zero exit status 1.

I encountered the same issue.

[hhuang-code]

I am trying to run OmegaFold on Google collab, but with the test sequence I always get this error:

ModuleNotFoundError: No module named 'Bio.Data.SCOPData' CalledProcessError Traceback (most recent call last) in <cell line: 42>() 40 out.write(f">{ID}\n{sequence}\n") 41 ---> 42 get_ipython().run_line_magic('shell', 'python OmegaFold/main.py --offset_rope={offset_rope} --device={device} --subbatch_size={subbatch_size} --num_cycle={num_cycle} {ID}.fasta .') 43 44 def renum_pdb_str(pdb_str, Ls=None, renum=True, offset=1): 2 frames /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 'python OmegaFold/main.py --offset_rope=False --device=cuda --subbatch_size=500 --num_cycle=4 test_a5e17.fasta .' returned non-zero exit status 1.

I encountered the same issue.

Installing biopython==1.78 resolved this issue.

[dasterix]

It looks like SCOPdata was deprecated and replaced with a new module: https://github.com/biopython/biopython/commit/257143be9196b77619d3d8cadc22039212681e08 The installation code needs to be updated to reflect this fact. Not sure if it would break other code in the package though

[OtakuOW]

Hi, I've been trying to understand for days now why Google Collabora no longer works for me. I can no longer create my Loras because Collab at a certain point gives me an error. I will post some photos soon, hoping to solve this problem :(

[OtakuOW]

[OtakuOW]

other: 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.

tf-keras 2.15.1 requires tensorflow<2.16,>=2.15, but you have tensorflow 2.16.1 which is incompatible.

torchaudio 2.2.1+cu121 requires torch==2.2.1, but you have torch 2.1.0 which is incompatible.

torchtext 0.17.1 requires torch==2.2.1, but you have torch 2.1.0 which is incompatible.