A problem realted to t000_ss2.

[Luckken21]

(RFAA1) [2200012187@hr-6-6-login RoseTTAFold-All-Atom]$ python -m rf2aa.run_inference --config-name protein /gpfs/share/home/2200012187/mambaforge/envs/RFAA1/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, 1.58sequences/s] Running HHblits against UniRef30 with E-value cutoff 1e-10

• 07:49:51.566 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m

• 07:49:51.566 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov75.a3m

• 07:49:51.746 WARNING: Maximum number 100000 of sequences exceeded in file 7u7wprotein/A/hhblits/t000.1e-10.a3m

• 07:50:30.457 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m

• 07:50:30.457 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov50.a3m

• 07:50:30.638 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 I try to run the 7u7wprotein, but why the programm cannot find t000.ss2? Thanks a lot if you can help me!

[caicaiandfeifei]

I met the same problem, and felt confused.I'm trying to reinstall PSIPRED, but it doesn't really work

[dirrei]

I had the same issue and for me 'input_prep/make_ss.sh' was not set as executable. This could be fixed with a simple: chmod 755 input_prep/make_ss.sh Hope that helps.

[Luckken21]

I have solved the problem by using dirrei's method. Thanks a lot!

[Yang-Wang-2020]

Same here. The psipred issue was solved using dirrei's method. Thanks a lot!