I'm getting the following error when I try to run the affinity prediction. This is trying to run the example affinity yaml. Other the ligand yaml ran fine.
Checking input data for affinity.
Running affinity prediction for 1 input.
Traceback (most recent call last):
File "/opt/conda/bin/boltz", line 8, in
sys.exit(cli())
File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/sagemaker-user/boltz2/boltz/src/boltz/main.py", line 1391, in predict
model_module = Boltz2.load_from_checkpoint(
File "/opt/conda/lib/python3.10/site-packages/pytorch_lightning/utilities/model_helpers.py", line 125, in wrapper
return self.method(cls, *args, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/pytorch_lightning/core/module.py", line 1581, in load_from_checkpoint
loaded = _load_from_checkpoint(
File "/opt/conda/lib/python3.10/site-packages/pytorch_lightning/core/saving.py", line 63, in _load_from_checkpoint
checkpoint = pl_load(checkpoint_path, map_location=map_location)
File "/opt/conda/lib/python3.10/site-packages/lightning_fabric/utilities/cloud_io.py", line 60, in _load
return torch.load(
File "/opt/conda/lib/python3.10/site-packages/torch/serialization.py", line 1491, in load
with _open_zipfile_reader(opened_file) as opened_zipfile:
File "/opt/conda/lib/python3.10/site-packages/torch/serialization.py", line 771, in init
super().init(torch._C.PyTorchFileReader(name_or_buffer))
RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory
The affinity checkpoint that was downloaded (boltz2_aff.ckpt) didn't work properly. I tried a different version of the checkpoint and it works now.
jwohlwend
