Error while using AlphaFold for predicted structure

Dear ColabFold developers,

I faced some errors while trying to predict protein structures. Finally, I obtained a predicted structure so alphafold ran normally. However, i was not able to have the pdb file. I am just wondering if these errors will have a major effect on the prediction or not?

Thank you so much for your help,

Best regrards,

Here are the errors :

NameError Traceback (most recent call last)
in
40 # --- Search against genetic databases ---
41
---> 42 I = cf_af.prep_msa(I, msa_method, add_custom_msa, msa_format,
43 pair_mode, pair_cov, pair_qid, TMP_DIR=TMP_DIR)
44 mod_I = I
NameError: name 'cf_af' is not defined

NameError Traceback (most recent call last)

in
11 #https://github.com/markdown - qid minimum sequence identity with query (%)
12
---> 13 mod_I = cf_af.prep_filter(I, trim, trim_inverse, cov, qid)
14
15 if I["msas"] != mod_I["msas"]:

NameError: name 'cf_af' is not defined

NameError Traceback (most recent call last)

in
16 #https://github.com/markdown - For example, sequence:ABC:DEF, homooligomer: 2:1, the first protein ABC will be modeled as a homodimer (2 copies) and second DEF a monomer (1 copy).
17
---> 18 I = cf_af.prep_inputs(sequence, jobname, homooligomer, clean=IN_COLAB)
NameError: name 'cf_af' is not defined

NameError Traceback (most recent call last)

in
38
39 # prep input features
---> 40 feature_dict = cf_af.prep_feats(mod_I, clean=IN_COLAB)
41 Ls_plot = feature_dict["Ls"]
42

NameError: name 'cf_af' is not defined

in
6
7 # add settings file
----> 8 settings_path = os.path.join(I["output_dir"],"settings.txt")
9 with open(settings_path, "w") as text_file:
10 text_file.write(f"notebook=https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced_beta.ipynb\n")

NameError: name 'os' is not defined

Start by running the AlphaFold2_advanced_beta.ipynb notebook and inspect the cells reporting that cf_af and os are undefined. Determine whether the errors prevent the predicted structure from being written, then verify whether a PDB file is produced and whether the prediction completes successfully.