Issue with Stack overflow at the Run Prediction cell

Expected Behavior: Initiation of the "run prediction" algorithm on the AlphaFold2.ipynb web application.

Current Behavior: Gives an error saying "Stack Overflow" immediately after initiation.

Steps to Reproduce (for bugs):

Initially I thought it was because I had entered a set of sequences that was too ambitious, but the problem occurred with sequences I had already evaluated. Any set of sequences I input, however small, cause this error by the "Run Prediction" cell. It was working yesterday and earlier today, and stopped.

ColabFold Output (for bugs)

#@title Run Prediction
import sys
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)

from colabfold.download import download_alphafold_params, default_data_dir
from colabfold.utils import setup_logging
from colabfold.batch import get_queries, run, set_model_type
import os
try:
K80_chk = os.popen('nvidia-smi | grep "Tesla K80" | wc -l').read()
except:
K80_chk = "0"
pass
if "1" in K80_chk:
print("WARNING: found GPU Tesla K80: limited to total length < 1000")
if "TF_FORCE_UNIFIED_MEMORY" in os.environ:
del os.environ["TF_FORCE_UNIFIED_MEMORY"]
if "XLA_PYTHON_CLIENT_MEM_FRACTION" in os.environ:
del os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"]

from colabfold.colabfold import plot_protein
from pathlib import Path
import matplotlib.pyplot as plt

For some reason we need that to get pdbfixer to import

if use_amber and f"/usr/local/lib/python{python_version}/site-packages/" not in sys.path:
sys.path.insert(0, f"/usr/local/lib/python{python_version}/site-packages/")

def prediction_callback(unrelaxed_protein, length, prediction_result, input_features, type):
fig = plot_protein(unrelaxed_protein, Ls=length, dpi=150)
plt.show()
plt.close()

result_dir="."
if 'logging_setup' not in globals():
setup_logging(Path(".").joinpath("log.txt"))
logging_setup = True

queries, is_complex = get_queries(queries_path)
model_type = set_model_type(is_complex, model_type)
download_alphafold_params(model_type, Path("."))
run(
queries=queries,
result_dir=result_dir,
use_templates=use_templates,
custom_template_path=custom_template_path,
use_amber=use_amber,
msa_mode=msa_mode,
model_type=model_type,
num_models=5,
num_recycles=num_recycles,
model_order=[1, 2, 3, 4, 5],
is_complex=is_complex,
data_dir=Path("."),
keep_existing_results=False,
recompile_padding=1.0,
rank_by="auto",
pair_mode=pair_mode,
stop_at_score=float(100),
prediction_callback=prediction_callback,
dpi=dpi,
zip_results=True
)
os.system(f"unzip {jobname}.result.zip")

UnicodeEncodeError Traceback (most recent call last)
in
42 model_type = set_model_type(is_complex, model_type)
43 download_alphafold_params(model_type, Path("."))
---> 44 run(
45 queries=queries,
46 result_dir=result_dir,
/usr/local/lib/python3.8/dist-packages/colabfold/batch.py in run(queries, result_dir, num_models, num_recycles, model_order, is_complex, num_ensemble, model_type, msa_mode, use_templates, custom_template_path, use_amber, keep_existing_results, rank_by, pair_mode, data_dir, host_url, random_seed, stop_at_score, recompile_padding, recompile_all_models, zip_results, prediction_callback, save_single_representations, save_pair_representations, training, use_gpu_relax, stop_at_score_below, dpi, max_msa)
1270 )
1271
-> 1272 bibtex_file = write_bibtex(
1273 model_type, use_msa, use_env, use_templates, use_amber, result_dir
1274 )

/usr/local/lib/python3.8/dist-packages/colabfold/citations.py in write_bibtex(model, use_msa, use_env, use_templates, use_amber, result_dir, bibtex_file)
129 with bibtex_file.open("w") as writer:
130 for i in to_cite:
--> 131 writer.write(citations[i])
132 writer.write("\n")
133

UnicodeEncodeError: 'ascii' codec can't encode character '\xfc' in position 53: ordinal not in range(128)

Context

As stated above, no set of sequences will work.

Your Environment

I used the web application, from an up-to-date Google Chrome browser, on a Windows 10 laptop.

• Git commit used
• If you run it on a local system. Please add the server specifications
• Operating system and version:

Any help would be great.

Start by reproducing the Run Prediction cell in AlphaFold2.ipynb, then inspect colabfold/batch.py around run() and colabfold/citations.py in write_bibtex(), where the traceback points. Verify that the citation-writing step handles the non-ASCII character shown in the error and that prediction completes without the reported encoding failure.