Comments (4)
Hi Junhui,
This file should be copied over during the Docker build process as given in the Dockerfile:
https://github.com/deepmind/alphafold/blob/main/docker/Dockerfile#L60-L61
Is that not working?
(If you are setting up without using Docker I recommend following the Dockerfile to make sure you get all the steps and correct versions.)
from alphafold.
Oh, I was running it on a non docker cluster using the script run_alphafold.py
(since our HPC doesn't and will not support Docker container...). Thanks for clarifying!
from alphafold.
No problem! I believe there are some other issues discussing how to run it without Docker, if that helps.
from alphafold.
I had a similar problem on a non_docker install.
I noticed that the file failed to download due to a certificate error reported by wget. The command indicated on the website uses the -q
option. This option prevented the error from being reported.
The command for "Download chemical properties to the common folder" is indicated on the website:
wget -q -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
I just removed the -q
and used --no-check-certificate
. This solved my case:
wget --no-check-certificate -P alphafold/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
from alphafold.
Related Issues (20)
- Resource not found: pdb70_from_mmcif_200401.tar.gz HOT 1
- Install third-party software stalls at 17% HOT 1
- AlphaFold Stuck at hhblits Step on Cluster Compute Node
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- alphafold outputs only have msas HOT 4
- ImportError: cannot import name 'SCOPData' from 'Bio.Data' HOT 5
- docker.errors.APIError: 500 Server Error for http+docker://localhost/v1.43/containers/ee2565cd6294bdf23537e9fb81814d89cb240f8c02b23f24a0926e3c66b44aea/start: Internal Server Error ("could not select device driver "nvidia" with capabilities: [[gpu]]") HOT 2
- Can I debug the code in the pycharm? HOT 1
- HHblits query is running time too long! HOT 2
- Missing function in docker build
- RMSD95 Definition
- Calculation of ipTM score for multimers greater than a dimer
- Attention docstring missing head dimension for arguments mask and nonbatched_bias
- HMMER MSAs aren't saved and repeated when running with --use_precomputed_msas=True HOT 10
- bash redirection error HOT 1
- ` HHSearch failed` with no `stdout` or `stderr` output HOT 5
- JAX 0.4.14 jaxlib cudnn error - non-docker installation HOT 2
- 404 Client Error for http+docker://localhost/v1.44/images/create?tag=latest&fromImage=alphafold: Not Found ("pull access denied for alphafold, repository does not exist or may require 'docker login': denied: requested access to the resource is denied") HOT 6
- Downloading mmCIF files problem HOT 2
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