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baker-laboratory / RoseTTAFold-All-Atom

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A problem realted to t000_ss2. #106

Open Luckken21 opened 6 months ago

Luckken21 commented 6 months ago

(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

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 commented 6 months ago

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

dirrei commented 6 months ago

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 commented 6 months ago

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

Yang-Wang-2020 commented 5 months ago

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