FileNotFoundError: MSA file not found during prediction

[Arman-Salahshour]

I encountered an error while running boltz predict with the --use_msa_server flag. The error message indicates that an expected MSA file (test_18b28/test_18b28_0.a3m) is missing.

Command Executed:
boltz predict test_18b28/test_18b28.fasta --use_msa_server

Error Message:
Downloading the CCD dictionary to /root/.boltz/ccd.pkl. You may change the cache directory with the --cache flag.
Downloading the model weights to /root/.boltz/boltz1_conf.ckpt. You may change the cache directory with the --cache flag.
Checking input data.
Running predictions for 1 structure
Processing input data.
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/miniconda/bin/boltz", line 8, in
sys.exit(cli())
^^^^^
File "/miniconda/lib/python3.12/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/miniconda/lib/python3.12/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/miniconda/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/miniconda/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/miniconda/lib/python3.12/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/miniconda/lib/python3.12/site-packages/boltz/main.py", line 613, in predict
process_inputs(
File "/miniconda/lib/python3.12/site-packages/lightning_utilities/core/rank_zero.py", line 42, in wrapped_fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/miniconda/lib/python3.12/site-packages/boltz/main.py", line 416, in process_inputs
raise e
File "/miniconda/lib/python3.12/site-packages/boltz/main.py", line 379, in process_inputs
raise FileNotFoundError(msg)
FileNotFoundError: MSA file test_18b28/test_18b28_0.a3m not found.

1. Does --use_msa_server automatically generate the required MSA file, or should it be created manually beforehand?
2. If the MSA file should be auto-generated, could this error be related to a server issue or an incorrect dependency?
3. Are there any specific dependencies or configurations needed to enable automatic MSA file generation?

Any guidance on resolving this issue would be greatly appreciated!