Error in the protein example

[ILUT1]

I already solved problem #17 about UniRef30 database. (by changing folder name UniRef30 into uniclust and changing UniRef30_2021_06 into UniRef30_2020_06 in make_msa.sh)

However, I got another error while running the protein example.

$ ~/mambaforge/envs/RFAA/bin/python -m rf2aa.run_inference --config-name protein ~/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein': 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/7u7w_A.fasta 7u7w_protein/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03 Predicting: 100%|█████████████████████████████████████████████████| 1/1 [00:00<00:00, 2.90sequences/s] Running HHblits against UniRef30 with E-value cutoff 1e-10

• 11:15:12.435 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m

• 11:15:12.435 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov75.a3m

• 11:15:12.522 WARNING: Maximum number 100000 of sequences exceeded in file 7u7wprotein/A/hhblits/t000.1e-10.a3m

• 11:15:28.884 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m

• 11:15:28.884 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov50.a3m

• 11:15:28.970 WARNING: Maximum number 100000 of sequences exceeded in file 7u7wprotein/A/hhblits/t000.1e-10.a3m

Running PSIPRED Running hhsearch cat: 7u7wprotein/A/t000.ss2: No such file or directory

Should I modify other things?

[cyangNYU]

Take a look at your input_prep/make_ss.sh file, check if it is executable. If not, chmod +x input_prep/make_ss.sh.

[gzlabzzh]

Take a look at your input_prep/make_ss.sh file, check if it is executable. If not, chmod +x input_prep/make_ss.sh.

I can't find "input_prep/make_ss.sh" in RoseTTAFold-All-Aton folder. Can you tell me where is it?

[xie-yun-ai]

Take a look at your input_prep/make_ss.sh file, check if it is executable. If not, chmod +x input_prep/make_ss.sh.

I can't find "input_prep/make_ss.sh" in RoseTTAFold-All-Aton folder. Can you tell me where is it?

Hello, the input_prep is just below after you unzip rosettafold all atom. If you don't have it, the compressed package you downloaded may be incomplete

[ILUT1]

Take a look at your input_prep/make_ss.sh file, check if it is executable. If not, chmod +x input_prep/make_ss.sh.

Thanks, it works well! I also encountered the problem of #34.