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Hi all:
When I try to run python3 docker/run_docker.py --fasta_paths=gfp.fasta --max_template_date=2024-12-30 --data_dir=/media/1E8E7BAA8E7B795B/database/ --db_preset=reduced_dbs --output_dir=/home/CD47/
I got the following issues:
I1231 17:50:01.220709 129183842236224 run_docker.py:116] Mounting /home/gaon/alphafold -> /mnt/fasta_path_0
I1231 17:50:01.221176 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/uniref90 -> /mnt/uniref90_database_path
I1231 17:50:01.221523 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/mgnify -> /mnt/mgnify_database_path
I1231 17:50:01.221757 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database -> /mnt/data_dir
I1231 17:50:01.222091 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
I1231 17:50:01.222338 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/pdb_mmcif -> /mnt/obsolete_pdbs_path
I1231 17:50:01.222602 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/pdb70 -> /mnt/pdb70_database_path
I1231 17:50:01.222913 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/small_bfd -> /mnt/small_bfd_database_path
Traceback (most recent call last):
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/home/gaon/miniconda3/lib/python3.11/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: http+docker://localhost/v1.47/containers/create
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/containers.py", line 811, in run
container = self.create(image=image, command=command,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/containers.py", line 870, in create
resp = self.client.api.create_container(**create_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/container.py", line 430, in create_container
return self.create_container_from_config(config, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/container.py", line 441, in create_container_from_config
return self._result(res, True)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 274, in _result
self._raise_for_status(response)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.ImageNotFound: 404 Client Error for http+docker://localhost/v1.47/containers/create: Not Found ("No such image: alphafold:latest")
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/home/gaon/miniconda3/lib/python3.11/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: http+docker://localhost/v1.47/images/create?tag=latest&fromImage=alphafold
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gaon/alphafold/docker/run_docker.py", line 267, in
app.run(main)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
^^^^^^^^^^
File "/home/gaon/alphafold/docker/run_docker.py", line 237, in main
container = client.containers.run(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/containers.py", line 814, in run
self.client.images.pull(image, platform=platform)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/images.py", line 446, in pull
pull_log = self.client.api.pull(
^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/image.py", line 430, in pull
self._raise_for_status(response)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.APIError: 500 Server Error for http+docker://localhost/v1.47/images/create?tag=latest&fromImage=alphafold: Internal Server Error ("Get "https://registry-1.docker.io/v2/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)")
I used docker images
And this is my output:
'''
REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold latest 5ea074d4fce3 38 minutes ago 11.4GB
nvidia/cuda 12.2.0-base-ubuntu22.04 00d989b22f26 13 months ago 239MB
hello-world latest d2c94e258dcb 20 months ago 13.3kB
’‘’
But when I check python I found that I could not see the images in python which looks like that :
[<Image: ''>, <Image: 'hello-world:latest'>, <Image: 'ubuntu:xenial'>]
Any help would be appreciated.
The text was updated successfully, but these errors were encountered:
Hi all:
When I try to run python3 docker/run_docker.py --fasta_paths=gfp.fasta --max_template_date=2024-12-30 --data_dir=/media/1E8E7BAA8E7B795B/database/ --db_preset=reduced_dbs --output_dir=/home/CD47/
I got the following issues:
I1231 17:50:01.220709 129183842236224 run_docker.py:116] Mounting /home/gaon/alphafold -> /mnt/fasta_path_0
I1231 17:50:01.221176 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/uniref90 -> /mnt/uniref90_database_path
I1231 17:50:01.221523 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/mgnify -> /mnt/mgnify_database_path
I1231 17:50:01.221757 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database -> /mnt/data_dir
I1231 17:50:01.222091 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
I1231 17:50:01.222338 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/pdb_mmcif -> /mnt/obsolete_pdbs_path
I1231 17:50:01.222602 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/pdb70 -> /mnt/pdb70_database_path
I1231 17:50:01.222913 129183842236224 run_docker.py:116] Mounting /media/gaon/1E8E7BAA8E7B795B/database/small_bfd -> /mnt/small_bfd_database_path
Traceback (most recent call last):
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/home/gaon/miniconda3/lib/python3.11/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: http+docker://localhost/v1.47/containers/create
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/containers.py", line 811, in run
container = self.create(image=image, command=command,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/containers.py", line 870, in create
resp = self.client.api.create_container(**create_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/container.py", line 430, in create_container
return self.create_container_from_config(config, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/container.py", line 441, in create_container_from_config
return self._result(res, True)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 274, in _result
self._raise_for_status(response)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.ImageNotFound: 404 Client Error for http+docker://localhost/v1.47/containers/create: Not Found ("No such image: alphafold:latest")
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/home/gaon/miniconda3/lib/python3.11/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: http+docker://localhost/v1.47/images/create?tag=latest&fromImage=alphafold
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gaon/alphafold/docker/run_docker.py", line 267, in
app.run(main)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
^^^^^^^^^^
File "/home/gaon/alphafold/docker/run_docker.py", line 237, in main
container = client.containers.run(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/containers.py", line 814, in run
self.client.images.pull(image, platform=platform)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/models/images.py", line 446, in pull
pull_log = self.client.api.pull(
^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/image.py", line 430, in pull
self._raise_for_status(response)
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/miniconda3/lib/python3.11/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.APIError: 500 Server Error for http+docker://localhost/v1.47/images/create?tag=latest&fromImage=alphafold: Internal Server Error ("Get "https://registry-1.docker.io/v2/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)")
I used docker images
And this is my output:
'''
REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold latest 5ea074d4fce3 38 minutes ago 11.4GB
nvidia/cuda 12.2.0-base-ubuntu22.04 00d989b22f26 13 months ago 239MB
hello-world latest d2c94e258dcb 20 months ago 13.3kB
’‘’
But when I check python I found that I could not see the images in python which looks like that :
[<Image: ''>, <Image: 'hello-world:latest'>, <Image: 'ubuntu:xenial'>]
Any help would be appreciated.
The text was updated successfully, but these errors were encountered: