I've tried to use FastFold for a large hetero-multimer protein complex, but I encountered this issue.
2023-07-25 14:53:20,908 INFO worker.py:1518 -- Started a local Ray instance.
2023-07-25 14:53:22,253 INFO workflow_access.py:356 -- Initializing workflow manager...
2023-07-25 14:53:24,072 INFO api.py:203 -- Workflow job created. [id="fastfold_data_workflow Tue Jul 25 14:53:22 2023"].
[2m[36m(WorkflowManagementActor pid=1387)[0m 2023-07-25 14:53:24,128 INFO workflow_executor.py:86 -- Workflow job [id=fastfold_data_workflow Tue Jul 25 14:53:22 2023] started.
...
<MSA generation was successfully finished>
...
...
running in multimer mode...
Traceback (most recent call last):
File "/foo/bar/FastFold/inference.py", line 556, in <module>
main(args)
File "/foo/bar/FastFold/inference.py", line 164, in main
inference_multimer_model(args)
File "/foo/bar/FastFold/inference.py", line 285, in inference_multimer_model
processed_feature_dict = feature_processor.process_features(
File "/foo/bar/FastFold/fastfold/data/feature_pipeline.py", line 124, in process_features
return np_example_to_features(
File "/foo/bar/FastFold/fastfold/data/feature_pipeline.py", line 106, in np_example_to_features
features = input_pipeline_fn(tensor_dict, cfg.common, cfg[mode])
File "/foo/bar/FastFold/fastfold/data/input_pipeline_multimer.py", line 107, in process_tensors_from_config
tensors = compose(nonensembled)(tensors)
File "/foo/bar/FastFold/fastfold/data/data_transforms.py", line 76, in <lambda>
return lambda x: f(x, *args, **kwargs)
File "/foo/bar/FastFold/fastfold/data/input_pipeline_multimer.py", line 124, in compose
x = f(x)
File "/foo/bar/FastFold/fastfold/data/data_transforms_multimer.py", line 298, in make_msa_profile
batch['msa_mask'][..., None],
KeyError: 'msa_mask'
I've tried to use FastFold for a large hetero-multimer protein complex, but I encountered this issue.
I know this issue is similar to https://github.com/hpcaitech/FastFold/issues/119, but I have no idea for the latest FastFold version. Please let me know the solution.
Computational environment
The input command was: