I am trying to run AF-multimer and my script ran for about 3ish hours and I get the following error. Not sure how to resolve this and would appreciate any advice.
Adding to the above error, my results folder is empty with just two files, features.pkl msas. This is my first time running AF-multimer locally and would appreciate the help.
Hi,
I am trying to run AF-multimer and my script ran for about 3ish hours and I get the following error. Not sure how to resolve this and would appreciate any advice.
singularity exec --nv -B /scratch/groups/ $alphafold_singularity \ python $alphafold_run \ --model_preset=multimer \ --data_dir=/scratch/groups/ \ --fasta_paths=/scratch/groups/EGFRvIII.fasta \ --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 \ --max_template_date=2022-1-1 \ --db_preset=reduced_dbs \ --small_bfd_database_path=/scratch/groups/small_bfd/bfd-first_non_consensus_sequences.fasta \ --pdb_seqres_database_path=/scratch/groups/pdb_seqres/pdb_seqres.txt \ --uniprot_database_path=/scratch/groups/uniprot/uniprot.fasta
Thank you in advance.