Alphafold2.3.2 not working: Could not find HHsearch database /shared/bank/alphafold2/current/2.3/pdb70/pdb70

IFB Core Cluster
1

Hello IFB team,

I am unable to run Alphafold2.3.2 for monomer structures due to this error message: raise ValueError(f'Could not find HHsearch database {database_path}')
ValueError: Could not find HHsearch database /shared/bank/alphafold2/current/2.3/pdb70/pdb70
srun: error: gpu-node-02: task 0: Exited with exit code 1

This error came from the script that was working earlier, below is my script:

#!/bin/bash

#SBATCH --partition=gpu
#SBATCH --gres=gpu:3g.20gb:1
#SBATCH --cpus-per-task=10
#SBATCH --mem=50G
#SBATCH --account=ancest_or_
#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/ancest_or_/AncOR24_25_node189.fasta,AncOR35_36_node413.fasta
--output_dir=/shared/projects/ancest_or_
--model_preset=monomer
--db_preset=full_dbs
--data_dir=/shared/bank/alphafold2/current/2.3
--uniref90_database_path=/shared/bank/alphafold2/current/2.3/uniref90/uniref90.fasta
--mgnify_database_path=/shared/bank/alphafold2/current/2.3/mgnify/mgy_clusters_2018_12.fa
--pdb70_database_path=/shared/bank/alphafold2/current/2.3/pdb70/pdb70
--template_mmcif_dir=/shared/bank/alphafold2/current/2.3/pdb_mmcif/mmcif_files
--max_template_date=2020-05-14
--obsolete_pdbs_path=/shared/bank/alphafold2/current/2.3/pdb_mmcif/obsolete.dat
--bfd_database_path=/shared/bank/alphafold2/current/2.3/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 \

I also tried changing my script to the current documetation avaible to run : AlphaFold - IFB Core Cluster Documentation

but then again I encounterd the same error : raise ValueError(f'Coucouldfind HHsearch database {database_path}')
ValueError: Could not find HHsearch database BANK_PATH/pdb70/pdb70

Therefore, I request if you could please help me with this issue? I am created this topic now because I had no news for the same query on my email and its been quite some time, I would really appreciite if you copuld help

Thanking you

Have a ncie day!

2

I want to point out that there was a typing mistake: I am unable to run Alphafold2.3.2, which is actually,2.2.3 not 2.3.2 while writing, but the script is alright.

second thing, this morning I tried to troubleshoot again but then I came across this message that I cannot submit any jobs on the cluster, I tried with different nodes but nothing works.

The Error message:

abaruah@clust-slurm-client2:/shared/projects/ancest_or_$ sbatch anestor_paralogs.sh

sbatch: error: Batch job submission failed: Requested node configuration is not available

I kindly request IFB team, to please help with this issue.

Thanking you

Have a good day!
Abhinob