Input Notebook: ColabDesign/esm_msa/example.ipynb
Output Notebook: /root/working_dir/ColabDesign_esm_msa_example.ipynb
Executing: 0% 0/7 [00:00<?, ?cell/s]Executing notebook with kernel: python3
Executing: 14% 1/7 [00:00<00:04, 1.40cell/s]
Executing: 43% 3/7 [00:01<00:02, 1.74cell/s]
Executing: 57% 4/7 [00:02<00:01, 1.74cell/s]
Traceback (most recent call last):
File "/usr/local/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill
execute_notebook(
File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [3]":
[NbConvertApp] Converting notebook /root/working_dir/ColabDesign_esm_msa_example.ipynb to html
[NbConvertApp] Writing 277496 bytes to /root/working_dir/ColabDesign_esm_msa_example.html
[NbConvertApp] Converting notebook /root/working_dir/ColabDesign_esm_msa_example.ipynb to asciidoc
/usr/local/lib/python3.10/dist-packages/nbconvert/utils/pandoc.py:51: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
check_pandoc_version()
[NbConvertApp] Writing 1307 bytes to /root/working_dir/ColabDesign_esm_msa_example.asciidoc
----------------------------------------------------------------
An Exception was encountered at `In [3]'.
+*In[1]:*+
[source, ipython3]
----
import os
if not os.path.exists("colabdesign"):
os.system("pip -q install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1")
os.system("ln -s /usr/local/lib/python3.7/dist-packages/colabdesign colabdesign")
os.system("curl -fsSL https://files.ipd.uw.edu/krypton/esm_msa_jax_v1.pkl.gz | gunzip > esm_msa.pkl")
----
+*In[2]:*+
[source, ipython3]
----
from colabdesign import esm_msa
import numpy as np
import jax
import matplotlib.pyplot as plt
----
[#papermill-error-cell]#Execution using papermill encountered an
exception here and stopped:#
+*In[3]:*+
[source, ipython3]
----
%shell wget -qnc https://github.com/sokrypton/ColabDesign/raw/v1.1.1/esm_msa/test_msa.npy
tokens = np.load('test_msa.npy')[0]
print(tokens.shape)
plt.figure()
plt.imshow(tokens)
plt.show()
----
+*Out[3]:*+
----
UsageError: Line magic function `%shell` not found.
----
+*In[ ]:*+
[source, ipython3]
----
model, alphabet = esm_msa.pretrained.get_model()
_ = model.init(model.key, tokens)
model.load_params('esm_msa.pkl')
----
+*In[ ]:*+
[source, ipython3]
----
result = model(tokens)
print(result.keys())
----
+*In[ ]:*+
[source, ipython3]
----
contacts = result['contacts']
plt.figure()
plt.imshow(contacts)
plt.show()
----