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The code stops at the protein example. #37

Open YOtani11517 opened 6 months ago

YOtani11517 commented 6 months ago

Thank you for your fantastic works, but I cannot run protein example. I tried change directory name by mv UniRef30 uniclust, replace "DB_UR30="$PIPE_DIR/uniclust/UniRef30_2021_06" to "DB_UR30="$PIPE_DIR/uniclust/UniRef30_2020_06" in make_msa.sh , add export BLASTMAT=$PIPE_DIR/blast-2.2.26/data/ to input_prep/make_ss.sh and do chmod +x input_prep/make_ss.sh. #33 #17 However, when I run python -m rf2aa.run_inference --config-name protein, script returned only =>

██████████/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)

Predicting: 0%| | 0/1 [00:00<?, ?sequences/s] Predicting: 100%|██████████| 1/1 [00:00<00:00, 1.09sequences/s] Predicting: 100%|██████████| 1/1 [00:00<00:00, 1.09sequences/s] Running HHblits against UniRef30 with E-value cutoff 1e-10

How to solve this problem. Thank you.

abhinavb22 commented 6 months ago

I have the same problem. Its been 2 days not and it is stuck like this: 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, 2.68sequences/s] Running HHblits against UniRef30 with E-value cutoff 1e-10

Amy-Fernandez commented 6 months ago

I had the same problem but the code runs with my own jobs. Have you tried your own job yet?

abhinavb22 commented 6 months ago

@Amy-Fernandez Yes I did try but still doesnt work:

Using the cif atom ordering for TRP. ./make_msa.sh examples/coa6.fasta coa6/A 12 16 pdb100_2021Mar03/pdb100_2021Mar03 Predicting: 100%|██████████████████████████| 1/1 [00:00<00:00, 2.86sequences/s] Running HHblits against UniRef30 with E-value cutoff 1e-10

kaistsystemsbiology commented 6 months ago

I've solved the problem by providing permission to the file "./input_prep/make_ss.sh" ($ chmod 773 ./input_prep/make_ss.sh). But I've got another problem regarding hhsearch...

ZhuofanShen commented 5 months ago

I think it would be easier for people to correctly set up if the Uniclust folder path in README and make_msa.sh are consistent.

For README, uniref30 [46G] wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz mkdir -p uniclust tar xfz UniRef30_2020_06_hhsuite.tar.gz -C ./uniclust

For make_msa.sh, DB_UR30="$PIPE_DIR/uniclust/UniRef30_2020_06"