Too many command-line arguments : No space in the command

[Azjer2014]

Hello, I'm trying to run alphafold using the command indicated below. I'm getting the error "Too many command-line arguments". I made sure to remove all the spaces. I'm not sure why I still get this error. I would appreciate any help to figure out the problem.

singularity run --home /Alphafold/alphafold-2.2.0 -e alphafold.sif run_alphafold.py \
        --data_dir=/Alphafold/alphafold-2.2.0/data/ \
        --output_dir=/Alphafold/alphafold-2.2.0/my-files/output/ \
        --fasta_paths=/Alphafold/alphafold-2.2.0/my-files/input/wild-type.fasta \
        --pdb70_database_path=/Alphafold/alphafold-2.2.0/data/pdb70/ \
        --mgnify_database_path=/Alphafold/alphafold-2.2.0/data/mgnify/ \
        --uniref90_database_path=/Alphafold/alphafold-2.2.0/data/uniref90/ \
        --uniclust30_database_path=/Alphafold/alphafold-2.2.0/data/uniclust30/ \
        --bfd_database_path=/Alphafold/alphafold-2.2.0/data/bfd/ \
        --template_mmcif_dir=/Alphafold/alphafold-2.2.0/data/mmCIF/ \
        --obsolete_pdbs_path=/Alphafold/alphafold-2.2.0/data/pdb_mmcif/ \
        --max_template_date=2020-05-14 \
        --model_names=monomer

[yamule]

--model_names=monomer may be --model_preset=monomer.

[susheelbhanu]

Hi,

I'm running into the same issue and below is my command:

singularity run --home /scratch/users/sbusi/af2/alphafold/alphafold -B /scratch/users/sbusi/af2/alphafold/alphafold/data:/data -B .:/etc --pwd /scratch/users/sbusi/af2 --nv /scratch/users/sbusi/af2/af2-container/alphafold_2.2.3.sif run_alphafold.py \
--fasta_paths=${ALPHAFOLD_DATADIR}/h1.fa \
--output_dir=${ALPHAFOLD_DIR}/output_af2 \
--data_dir=${ALPHAFOLD_DATADIR} \
--uniref90_database_path=${ALPHAFOLD_DIR}/uniref90/uniref90.fasta \
--mgnify_database_path=${ALPHAFOLD_DIR}/mgnify/mgy_clusters_2018_12.fa \
--bfd_database_path=${ALPHAFOLD_DIR}/bfd \
--pdb70_database_path=${ALPHAFOLD_DIR}/pdb70 \
--template_mmcif_dir=${ALPHAFOLD_DIR}/pdb_mmcif/mmcif_files \
--obsolete_pdbs_path=${ALPHAFOLD_DIR}/pdb_mmcif/obsolete.dat \
--model_preset=monomer \
--max_template_date=2021-11-01 \
--use_gpu_relax=True \
--db_preset=full_dbs

Thanks for your input on this.

[Azjer2014]

--model_names=monomer may be --model_preset=monomer.

Using your suggested parameter gives a different error about using a wrong parameter. The parameters in my command are correct.

[Azjer2014]

I have not troubleshoot this error yet but I can see your command is pointing to the actual files in the databases (mine direct to folders) so I'm going to try your way to see if it works.

[yamule]

Using your suggested parameter gives a different error about using a wrong parameter. The parameters in my command are correct.

How about --model_names=model_1 then?

[jianxinwang]

I'm having the same issue. I looked at the file run_alphafold.py. It has lines like:

def main(argv): if len(argv) > 1: raise app.UsageError('Too many command-line arguments.')

Is this a bug? How can you expect just one argument and asked for more?