Running Alphafold2 Script Path error

Zibo_Li · Mai 3, 2023, 12:59

Bonjour,
After the database paths were changed for Alphafold2, by using the following script, I got the error like that. Do you have any idea what should I do? Thanks in advance!

module load alphafold/2.1.1

mkdir -p /tmp/$USER_alphafold

srun run_alphafold.sh --fasta_paths=/shared/projects/alucchemo/SlitGR71.fa,SlitGR72.fa,SlitGR73.fa,SlitGR74.fa \

--output_dir=/shared/projects/alucchemo \

--model_preset=monomer \

--db_preset=full_dbs \

--data_dir=/shared/bank/alphafold2/current \

--uniref90_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/uniref90/uniref90.fasta \

--mgnify_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/mgnify/mgy_clusters_2018_12.fa \

--pdb70_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb70/pdb70 \

--template_mmcif_dir=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/mmcif_files \

--max_template_date=2020-05-14 \

--obsolete_pdbs_path=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/obsolete.dat \

--bfd_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \

--uniclust30_database_path=/shared/bank/alphafold2/2022-09-21/uniclust30/uniclust30_2018_08/uniclust30_2018_08

Error
I0503 12:00:04.115088 47457781206720 templates.py:857] Using precomputed obsolete pdbs /shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/obsolete.dat.
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/bin/run_alphafold.py", line 427, in
app.run(main)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/bin/run_alphafold.py", line 379, in main
model_params = data.get_model_haiku_params(
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/alphafold/model/data.py", line 36, in get_model_haiku_params
with open(path, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/shared/bank/alphafold2/current/params/params_model_1.npz'
srun: error: gpu-node-03: task 0: Exited with exit code 1

dbenaben · Mai 3, 2023, 3:13

Could yout try with:

--data_dir=/shared/bank/alphafold2/2022-09-21/

Or maybe switch to alphafold/2.2.3 ?

Zibo_Li · Mai 4, 2023, 7:20

Hello,
Thanks for your suggestions! However, none works. The error like that
I0503 19:05:09.650084 46972099931840 templates.py:857] Using precomputed obsolete pdbs /shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/obsolete.dat.
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/bin/run_alphafold.py", line 427, in
app.run(main)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/bin/run_alphafold.py", line 379, in main
model_params = data.get_model_haiku_params(
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.1.1/lib/python3.8/site-packages/alphafold/model/data.py", line 36, in get_model_haiku_params
with open(path, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/shared/bank/alphafold2/2022-09-21/current/params/params_model_1.npz'
srun: error: gpu-node-03: task 0: Exited with exit code 1

After changing the version of Alphfold2, the error is
FATAL Flags parsing error: flag --use_gpu_relax=None: Flag --use_gpu_relax must have a value other than None.
Pass --helpshort or --helpfull to see help on flags.
srun: error: gpu-node-03: task 0: Exited with exit code 1

Thanking you for any further suggestions!

Best regards,
Zibo

Zibo_Li · Mai 4, 2023, 9:08

Hello again,
I tried the command line like this > *-data_dir=/shared/bank/alphafold2/current/2.3/2023-04-28 *
It seems to work.
But I am wondering if I want to change to use alphafold2 2.2.3 version, what should I do with my script? The script was changed to #SBATCH --gres=gpu:3g.20gb:1
But it doesnot work.

Thanks!

dbenaben · Mai 4, 2023, 9:52

Hello,

Thanks for your feedback.

For alphafold 2.2.3, as mentioned in the error you can try --use_gpu_relax=True in the command line (in run_alphafold.sh ... and not in SBATCH directive).

Zibo_Li · Mai 4, 2023, 12:22

Thanks for your suggestion! I am sorry I am new to it.
But you mean I should submit my script like this:
srun run_alphafold.sh --use_gpu_relax=True --fasta_paths=/shared/projects/
or
--use_gpu_relax=True run_alphafold.sh --fasta_paths=/shared/projects/

Thanks!

Best regards

dbenaben · Mai 4, 2023, 12:24

The first one:

srun run_alphafold.sh --use_gpu_relax=True --fasta_paths=/shared/projects/...

Zibo_Li · Mai 4, 2023, 12:40

Great! Thanks!
Have a good afternoon!

Zibo_Li · Mai 5, 2023, 7:34

Good morning,
I used the new version Alphafold2 2.2.3 for a batch 4 fasta files modelled in one job. Here is the script but I got only one 3D structure as output from one fasta file only and some errors. Could you please kindly give me some ideas? Thanks in advance!
#!/bin/bash

#SBATCH --partition=gpu
#SBATCH --gres=gpu:3g.20gb:1
#SBATCH --cpus-per-task=10
#SBATCH --mem=50G
#SBATCH --account=alucchemo
#SBATCH --time 36:00:00

module load alphafold/2.2.3

mkdir -p /tmp/$USER_alphafold

srun run_alphafold.sh --use_gpu_relax=True --fasta_paths=/shared/projects/alucchemo/SlitGR150.fa,SlitGR152.fa,SlitGR154.fa,SlitGR156.fa
--output_dir=/shared/projects/alucchemo
--model_preset=monomer
--db_preset=full_dbs
--data_dir=/shared/bank/alphafold2/current/2.3/2023-04-28
--uniref90_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/uniref90/uniref90.fasta
--mgnify_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/mgnify/mgy_clusters_2018_12.fa
--pdb70_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb70/pdb70
--template_mmcif_dir=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/mmcif_files
--max_template_date=2020-05-14
--obsolete_pdbs_path=/shared/bank/alphafold2/current/2.3/2023-04-28/pdb_mmcif/obsolete.dat
--bfd_database_path=/shared/bank/alphafold2/current/2.3/2023-04-28/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--uniclust30_database_path=/shared/bank/alphafold2/2022-09-21/uniclust30/uniclust30_2018_08/uniclust30_2018_08