Could not get MSA/templates for msa: [Errno 2] No such file or directory:

Current Behavior

While running ColabFold 1.5.5, we encountered a FileNotFoundError related to the MSA/templates file.
Below are the details of the error and the SLURM script used.

#SBATCH --partition=gpu
#SBATCH --constraint=v100
#SBATCH --mem=64G

source /programs/sbgrid.shrc
module load cuda/12.0
module load gcc/10.2.0

colabfold_batch --num-recycle 1
--random-seed 0
--model-type alphafold2_multimer_v3
--num-models 2
--max-msa 8:16
--zip
--templates
--custom-template-path template_path
--save-recycles
--disable-cluster-profile
--overwrite-existing-results
/msa_path/msa.a3m
/output_folder/

ColabFold Output (for bugs)

2024-07-26 15:26:48,678 Running colabfold 1.5.5 (1648d2335943f9a483b6a803ebaea3e76162c788)
2024-07-26 15:26:51,423 Running on GPU
2024-07-26 15:26:55,277 Found 8 citations for tools or databases
2024-07-26 15:26:55,370 Query 1/1: msa (length 296)
2024-07-26 15:26:56,803 Could not get MSA/templates for msa: [Errno 2] No such file or directory: '/template_path/r4dn.cif'
Traceback (most recent call last):
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py", line 1475, in run
= get_msa_and_templates(jobname, query_seqs_unique, unpaired_msa, result_dir, 'single_sequence', use_templates,
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py", line 794, in get_msa_and_templates
template_feature = mk_template(
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py", line 140, in mk_template
templates_result = template_featurizer.get_templates(
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/alphafold/data/templates.py", line 883, in get_templates
result = _process_single_hit(
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/alphafold/data/templates.py", line 727, in _process_single_hit
cif_string = _read_file(cif_path)
File "/programs/x86_64-linux/colabfold/1.5.5/colabfold-conda/lib/python3.10/site-packages/alphafold/data/templates.py", line 670, in _read_file
with open(path, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/template_path/r4dn.cif'
2024-07-26 15:26:56,822 Done

Context

I'm using a custom template and MSA. The MSA was obtained from MMseq, the .cif file contains( _entity_poly_seq and _pdbx_audit_revision_history.revision_date)

Environment

University cluster, no access to web server

My best guess is that is having issues with creating the msa for the template, but I don't know how to solve this.

Start with colabfold/batch.py and the traceback through alphafold/data/templates.py, using the provided SLURM command and custom-template-path setting. Reproduce the missing-file failure and determine what handling or documentation is needed so the custom .cif template is found successfully.