google-deepmind / google-deepmind/alphafold
'uniref30_database_path
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Description
Hi,
I am trying to run the predictions with new ver. 2.3.0 multimer
Although I have installed everything from scratch after removing the previous image of alphafold in docker and rebuilding new image still its not working the error message is
run_docker.py:258] FATAL Flags parsing error: Unknown command line flag 'uniref30_database_path'. Did you mean: uniref90_database_path ?
Directories are also mounted correctly
python3 docker/run_docker.py --fasta_paths=/mnt/DATABIG/monomers_new/NOS1.fasta --max_template_date=2023-01-01 --model_preset=monomer --db_preset full_dbs --data_dir=/mnt/DATABIG/databases/ --gpu_devices=1 --models_to_relax=best
I0302 11:27:01.387156 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/monomers_new -> /mnt/fasta_path_0
I0302 11:27:01.387369 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/uniref90 -> /mnt/uniref90_database_path
I0302 11:27:01.387476 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/mgnify -> /mnt/mgnify_database_path
I0302 11:27:01.387561 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases -> /mnt/data_dir
I0302 11:27:01.387643 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
I0302 11:27:01.387732 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0302 11:27:01.387845 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/pdb70 -> /mnt/pdb70_database_path
I0302 11:27:01.387944 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/uniref30 -> /mnt/uniref30_database_path
I0302 11:27:01.388038 139961187600192 run_docker.py:116] Mounting /mnt/DATABIG/databases/bfd -> /mnt/bfd_database_path
I0302 11:27:05.063709 139961187600192 run_docker.py:258] /opt/conda/lib/python3.7/site-packages/haiku/_src/data_structures.py:37: FutureWarning: jax.tree_structure is deprecated, and will be removed in a future release. Use jax.tree_util.tree_structure instead.
I0302 11:27:05.064102 139961187600192 run_docker.py:258] PyTreeDef = type(jax.tree_structure(None))
I0302 11:27:05.064320 139961187600192 run_docker.py:258] FATAL Flags parsing error: Unknown command line flag 'uniref30_database_path'. Did you mean: uniref90_database_path ?
I0302 11:27:05.064502 139961187600192 run_docker.py:258] Pass --helpshort or --helpfull to see help on flags.
Please help me in this regard
Thank you
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