Google collab error
irinasspider opened this issue · comments
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 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.
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.
It looks like SCOPdata was deprecated and replaced with a new module: biopython/biopython@257143b
The installation code needs to be updated to reflect this fact. Not sure if it would break other code in the package though
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 :(
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.