"ERROR: no model params defined" when running Cyclic Peptide Design notebook locally
f-meireles opened this issue · comments
Hi everyone,
I'm trying to run the cyclic_peptide_binder_design notebook you created locally but I'm running into this "no model params defined" issue. If I try to run it on Google Colab it works perfectly, so I guess it must be a version issue with my locally installed libraries, but I still haven't been able to figure out which one is causing the problem.
This is the error I get once I try running the AfDesign cell:
**File [~/ColabDesign_cyclic_binder/ColabDesign-cyclic-binder/colabdesign/af/design.py:92], in _af_design.run(self, num_recycles, num_models, sample_models, models, backprop, callback, model_nums, return_aux)
[90] # Inside the run method, before the assertion
[91] print(f"DEBUG: model_nums={model_nums}, num_models={num_models}, sample_models={sample_models}, models={models}")
---> [92] assert len(model_nums) > 0, f"ERROR: no model params defined. DEBUG: model_nums={model_nums}, num_models={num_models}, sample_models={sample_models}, models={models}"
[94] # loop through model params
[95] auxs = []
AssertionError: ERROR: no model params defined. DEBUG: model_nums=[], num_models=None, sample_models=None, models=[]**
I've added this debug bit after the error to try figuring out what is happening, and for some reason these variables are not being assigned when "_get_model_nums()" is called.
These are all the packages I've installed in the conda environment I'm using:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.1.0 pypi_0 pypi
aiohttp 3.9.1 py311h459d7ec_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
anyio 4.2.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
biopython 1.83 pypi_0 pypi
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py311hb755f60_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.2 pyhd8ed1ab_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py311hb3a22ac_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
chex 0.1.85 pypi_0 pypi
comm 0.2.1 pyhd8ed1ab_0 conda-forge
contextlib2 21.6.0 pypi_0 pypi
contourpy 1.2.0 pypi_0 pypi
cryptography 42.0.2 py311hcb13ee4_0 conda-forge
cycler 0.12.1 pypi_0 pypi
debugpy 1.8.0 py311hb755f60_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dm-haiku 0.0.12.dev0 pypi_0 pypi
dm-tree 0.1.8 pypi_0 pypi
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
etils 1.6.0 pypi_0 pypi
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
flax 0.8.0 pypi_0 pypi
fonttools 4.47.2 pypi_0 pypi
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
frozenlist 1.4.1 py311h459d7ec_0 conda-forge
fsspec 2024.2.0 pypi_0 pypi
google-auth 2.27.0 pyhca7485f_0 conda-forge
google-colab 1.0.0 pyh44b312d_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.0.1 pyha770c72_0 conda-forge
importlib_metadata 7.0.1 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.0 pyhd33586a_0 conda-forge
ipython 8.21.0 pyh707e725_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jax 0.4.23 pypi_0 pypi
jaxlib 0.4.23 pypi_0 pypi
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
jmp 0.0.4 pypi_0 pypi
joblib 1.3.2 pypi_0 pypi
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py311h38be061_3 conda-forge
jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.21.1 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.2 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.1 py311h38be061_0 conda-forge
jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.12.5 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.2 pyhd8ed1ab_0 conda-forge
jupyterlab 4.0.12 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.2 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.5 pypi_0 pypi
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libblas 3.9.0 21_linux64_openblas conda-forge
libcblas 3.9.0 21_linux64_openblas conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
liblapack 3.9.0 21_linux64_openblas conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 2.1.5 py311h459d7ec_0 conda-forge
matplotlib 3.8.2 pypi_0 pypi
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pypi_0 pypi
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
ml-collections 0.1.1 pypi_0 pypi
ml-dtypes 0.3.2 pypi_0 pypi
msgpack 1.0.7 pypi_0 pypi
multidict 6.0.5 py311h459d7ec_0 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.14.2 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
notebook 7.0.7 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numpy 1.26.3 py311h64a7726_0 conda-forge
openssl 3.2.1 hd590300_0 conda-forge
opt-einsum 3.3.0 pypi_0 pypi
optax 0.1.9 pypi_0 pypi
orbax-checkpoint 0.5.2 pypi_0 pypi
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 2.2.0 py311h320fe9a_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.2.0 pypi_0 pypi
pip 24.0 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
portpicker 1.6.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.19.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
protobuf 4.25.2 pypi_0 pypi
psutil 5.9.8 py311h459d7ec_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py3dmol 2.0.4 pypi_0 pypi
pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge
pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyopenssl 24.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.11.7 hab00c5b_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.4 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311h459d7ec_1 conda-forge
pyzmq 25.1.2 py311h34ded2d_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.33.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rich 13.7.0 pypi_0 pypi
rpds-py 0.17.1 py311h46250e7_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
scipy 1.12.0 pypi_0 pypi
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
tabulate 0.9.0 pypi_0 pypi
tensorstore 0.1.53 pypi_0 pypi
terminado 0.18.0 pyh0d859eb_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.1 pypi_0 pypi
tornado 6.3.3 py311h459d7ec_1 conda-forge
traitlets 5.14.1 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.20240106 pyhd8ed1ab_0 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023d h0c530f3_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 py311h459d7ec_0 conda-forge
zeromq 4.3.5 h59595ed_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
Please let me know if I should provide any other information.
Thank you very much in advance for your attention.
Best wishes,
Fernando
Just a follow up in case someone goes through the same thing: I did not realize that the params folder was not on the repo. I just downloaded them directly from the directories on the Google Colab notebook.