Failed to Run Example Using Docker with Error Message

[maxshen29]

When running the example with Docker, the following error occurs.
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root@74197cb9a68e:/app# genie3 run -c examples/binder_design/experiment.yaml
📝 Detailed log: /app/logs/runs/2026-05-14_07-49-05_run_binder_design_example/run.log
────────────────────────────────────────
🚀 Run started
Experiment: binder_design_example
Rootdir: examples/binder_design
────────────────────────────────────────
🧬 Generation
Status: generation WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
I0000 00:00:1778744948.237658 18214 port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0.
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
I0000 00:00:1778744948.924547 18214 port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0.
✅ Generation finished
Output: examples/binder_design
────────────────────────────────────────
📊 Generation Summary
📦 Outputs
Samples generated: 5
🧪 Sampling
Per-sample generation: 11.862s
Sampling elapsed: 59.309s
────────────────────────────────────────
🎉 Generate completed
🧪 Evaluation
✅ Evaluation finished
Results: examples/binder_design/results
────────────────────────────────────────
📊 Evaluation Summary
📦 Outputs
Structures generated: 5
Sequences generated: 5
Model outputs written: 0
⚙️ Setup
Inverse-fold model init: 0.747s elapsed
Fold model preload: 0.137s elapsed
Startup elapsed: 0.884s
🧬 Inverse Fold
Inverse fold elapsed: 1.185s
Per-sequence inverse fold: 0.237s
🧪 Fold
Fold elapsed: 1.706s (model=colabfold, models=5, recycles=20)
Per-sequence fold: 0.341s (model=colabfold, models=5, recycles=20)
────────────────────────────────────────
🎉 Evaluate completed
🧪 Evaluation
❌ Evaluate failed
Traceback (most recent call last):
File "/app/src/genie3/cli.py", line 317, in _handle_evaluate
evaluation_result = run_evaluation(
File "/app/src/genie3/evaluation/workflow.py", line 78, in run_evaluation
main(args)
File "/app/src/genie3/evaluation/workflow.py", line 158, in main
runner.reduce(version, problem_dir_str, verbose, extra_kwargs)
File "/app/src/genie3/evaluation/pipeline.py", line 574, in reduce
reducer.reduce(rootdir=rootdir, verbose=verbose)
File "/app/src/genie3/evaluation/reducer/base.py", line 453, in reduce
self._filter(results_dir)
File "/app/src/genie3/evaluation/reducer/binder.py", line 412, in _filter
df_complex = pd.read_csv(os.path.join(results_dir, 'info.csv'))
File "/usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
return mapping[engine](f, **self.options)
File "/usr/local/lib/python3.10/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
❌ Run failed. See log: /app/logs/runs/2026-05-14_07-49-05_run_binder_design_example/run.log
❌ Run failed
Traceback (most recent call last):
File "/app/src/genie3/cli.py", line 246, in _handle_run
_run_single_shot(args, child_env)
File "/app/src/genie3/cli.py", line 524, in _run_single_shot
_run_child_stage(
File "/app/src/genie3/cli.py", line 664, in _run_child_stage
subprocess.run(cmd, check=True, env=child_env)
File "/usr/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/usr/local/bin/genie3', 'evaluate', '--config', 'examples/binder_design/experiment.yaml', '--reduce']' returned non-zero exit status 1.
❌ Run failed. See log: /app/logs/runs/2026-05-14_07-49-05_run_binder_design_example/run.log