Here I get this for python -m rf2aa.run_inference --config-name protein_sm
with the example from the repository
/home/use/.conda/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein_sm': Defaults list is missing _self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information
warnings.warn(msg, UserWarning)
Using the cif atom ordering for TRP.
./make_msa.sh examples/protein/7qxr.fasta 7qxr/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03
Predicting: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 1.54sequences/s]
Running HHblits against UniRef30 with E-value cutoff 1e-10
remybonnav
commented
2 weeks ago
I am not sure what shoudl be the output of a run.
Here I get this for python -m rf2aa.run_inference --config-name protein_sm with the example from the repository
/home/use/.conda/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein_sm': Defaults list is missing
_self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information warnings.warn(msg, UserWarning) Using the cif atom ordering for TRP. ./make_msa.sh examples/protein/7qxr.fasta 7qxr/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03 Predicting: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 1.54sequences/s] Running HHblits against UniRef30 with E-value cutoff 1e-1016:27:22.840 INFO: Input file = 7qxr/A/hhblits/t000_.1e-10.a3m
16:27:22.840 INFO: Output file = 7qxr/A/hhblits/t000_.1e-10.id90cov75.a3m
16:27:22.965 WARNING: Maximum number 100000 of sequences exceeded in file 7qxr/A/hhblits/t000_.1e-10.a3m
16:29:52.494 INFO: Input file = 7qxr/A/hhblits/t000_.1e-10.a3m
16:29:52.494 INFO: Output file = 7qxr/A/hhblits/t000_.1e-10.id90cov50.a3m
16:29:52.617 WARNING: Maximum number 100000 of sequences exceeded in file 7qxr/A/hhblits/t000_.1e-10.a3m
Running PSIPRED Running hhsearch cat: 7qxr/A/t000_.ss2: No such file or directory
Then it finishes.
But I cannot find any pdb file output