ValueError: Could not find CIFs

[leonhardt913]

I have been setting up the alphafold2 along with Docker. When I came to step 8 for test, I put the command in .sh file and run, but the following errors occurs:

~/bin/alphafold$ cat run_alphafold.sh
python3 docker/run_docker.py \
  --fasta_paths=fastafiles/test_protein.fasta \
  --max_template_date=2023-12-30 \
  --data_dir=/data/disk4/alphafoldDB \
  --output_dir=~/project/3-alphafold2-output

~/bin/alphafold $ sh run_alphafold.sh
I0313 20:59:48.014863 139881018193024 run_docker.py:116] Mounting /home/wuqy/bin/alphafold/fastafiles -> /mnt/fasta_path_0
I0313 20:59:48.223854 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/uniref90 -> /mnt/uniref90_database_path
I0313 20:59:48.429889 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/mgnify -> /mnt/mgnify_database_path
I0313 20:59:48.430127 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB -> /mnt/data_dir
I0313 20:59:48.432076 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/pdb_mmcif -> /mnt/template_mmcif_dir
I0313 20:59:48.433026 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0313 20:59:48.434590 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/pdb70 -> /mnt/pdb70_database_path
I0313 20:59:48.436120 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/uniref30 -> /mnt/uniref30_database_path
I0313 20:59:48.437566 139881018193024 run_docker.py:116] Mounting /data/disk4/alphafoldDB/bfd -> /mnt/bfd_database_path
I0313 20:59:51.911179 139881018193024 run_docker.py:258] E0313 12:59:51.910264 139938819991360 templates.py:838] Could not find CIFs in /mnt/template_mmcif_dir/mmcif_files

I0313 20:59:51.911416 139881018193024 run_docker.py:258] Traceback (most recent call last):
I0313 20:59:51.911603 139881018193024 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 570, in <module>
I0313 20:59:51.911774 139881018193024 run_docker.py:258] app.run(main)
I0313 20:59:51.911936 139881018193024 run_docker.py:258] File "/opt/conda/lib/python3.10/site-packages/absl/app.py", line 312, in run
I0313 20:59:51.912092 139881018193024 run_docker.py:258] _run_main(main, args)
I0313 20:59:51.912245 139881018193024 run_docker.py:258] File "/opt/conda/lib/python3.10/site-packages/absl/app.py", line 258, in _run_main
I0313 20:59:51.912397 139881018193024 run_docker.py:258] sys.exit(main(argv))
I0313 20:59:51.912575 139881018193024 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 478, in main
I0313 20:59:51.912730 139881018193024 run_docker.py:258] template_featurizer = templates.HhsearchHitFeaturizer(
I0313 20:59:51.912881 139881018193024 run_docker.py:258] File "/app/alphafold/alphafold/data/templates.py", line 839, in __init__
I0313 20:59:51.913031 139881018193024 run_docker.py:258] raise ValueError(f'Could not find CIFs in {self._mmcif_dir}')
I0313 20:59:51.913180 139881018193024 run_docker.py:258] ValueError: Could not find CIFs in /mnt/template_mmcif_dir/mmcif_files

I have also reviewed issue #160 about the Singularity approach, but I am not familiar with it. Is there a feasible solution to address this issue based on the current Docker configuration?

[Ruibin-Liu]

Does anyone have found a solution?

[Ruibin-Liu]

For my case, the problem was that the CIF files in the pdb_mmcif/raw directories were not 'flatterned' because one gz file might be damaged. My solution was just to download the mmcif dataset again. Double check that there is a pdb_mmcif/mmcif_files directory before running the docker script.

[leonhardt913]

@Ruibin-Liu Thank you. I will try re-downloading the CIF files again. But it is very unstable to download this part and i believe the files might be damaged during the occasionally disconnect.

In addition, I wonder whether the CIF files should be in .gz or unzipped?