Open apal6 opened 6 months ago
Hi,
I am trying to run alphafold multimer using singularity and even after giving all the necessary flags, I get an error which I am not sure about. Would appreciate any help.
`export alphafold_singularity=/scratch/groups/alphafold_2.1.2.sif export alphafold_run=/scratch/groups/alphafold/run_alphafold.py export alphafold_data_dir=/scratch/groups/
singularity exec --nv $alphafold_singularity \ python $alphafold_run --model_preset=multimer \ --data_dir=/scratch/groups/alphafold \ --fasta_paths=/scratch/groups/EGFRvIII.fa \ --output_dir=/scratch/groups/results \ --use_gpu_relax=True \ --uniref90_database_path=/scratch/groups/uniref90/uniref90.fasta \ --mgnify_database_path=/scratch/groups/mgnify/mgy_clusters_2022_05.fa \ --template_mmcif_dir=/scratch/groups/pdb_mmcif/mmcif_files \ --obsolete_pdbs_path=/scratch/groups/pdb_mmcif/obsolete.dat \ --bfd_database_path=/scratch/groups/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ --max_template_date=2022-1-1 \ --db_preset=reduced_dbs \ --uniref30_database_path=/scratch/groups/uniref30/UniRef30_2021_03 \ --pdb_seqres_database_path=/scratch/groups/pdb_seqres/pdb_seqres.txt \ --uniprot_database_path=/scratch/groups/uniprot/uniprot.fasta `
Thank you!
Hi,
I am trying to run alphafold multimer using singularity and even after giving all the necessary flags, I get an error which I am not sure about. Would appreciate any help.
`export alphafold_singularity=/scratch/groups/alphafold_2.1.2.sif export alphafold_run=/scratch/groups/alphafold/run_alphafold.py export alphafold_data_dir=/scratch/groups/
singularity exec --nv $alphafold_singularity \ python $alphafold_run --model_preset=multimer \ --data_dir=/scratch/groups/alphafold \ --fasta_paths=/scratch/groups/EGFRvIII.fa \ --output_dir=/scratch/groups/results \ --use_gpu_relax=True \ --uniref90_database_path=/scratch/groups/uniref90/uniref90.fasta \ --mgnify_database_path=/scratch/groups/mgnify/mgy_clusters_2022_05.fa \ --template_mmcif_dir=/scratch/groups/pdb_mmcif/mmcif_files \ --obsolete_pdbs_path=/scratch/groups/pdb_mmcif/obsolete.dat \ --bfd_database_path=/scratch/groups/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ --max_template_date=2022-1-1 \ --db_preset=reduced_dbs \ --uniref30_database_path=/scratch/groups/uniref30/UniRef30_2021_03 \ --pdb_seqres_database_path=/scratch/groups/pdb_seqres/pdb_seqres.txt \ --uniprot_database_path=/scratch/groups/uniprot/uniprot.fasta `
Thank you!