google-deepmind / google-deepmind/alphafold

Failed to find source directory "/home/gpux1/alphafold/uniref90" to mount in Docker container.

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Python
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Description

Hi, everyone. I have followed all the steps as instructions, but when I execute the last step(I have just installed the reduced_dbs)
```
python3 docker/run_docker.py \
> --fasta_paths=T1050.fasta \
> --max_template_date=2020-05-14 \
> --model_preset=monomer \
> --db_preset=reduced_dbs \
> --data_dir=$DOWNLOAD_DIR \
> --output_dir=/home/user/absolute_path_to_the_output_dir
```
The traceback is as follows

```
File "/home/gpux1/alphafold/docker/run_docker.py", line 267, in
app.run(main)
File "/home/gpux1/miniconda3/lib/python3.11/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/gpux1/miniconda3/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
^^^^^^^^^^
File "/home/gpux1/alphafold/docker/run_docker.py", line 210, in main
mount, target_path = _create_mount(name, path)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gpux1/alphafold/docker/run_docker.py", line 114, in _create_mount
raise ValueError(f'Failed to find source directory "{source_path}" to '
ValueError: Failed to find source directory "/home/gpux1/alphafold/uniref90" to mount in Docker container.
```

Not sure how to fix this problem, is it need to install the uniref90 first?

Thanks!

Contributor guide

Open the contributing guide

Research direction

Start with docker/run_docker.py, especially _create_mount at line 114 and the database path assembled in main around line 210. Reproduce the reduced_dbs command with --data_dir and check how uniref90 is expected to be located; done means the invocation no longer fails with the missing-source-directory error.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
devops
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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