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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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About errors that occur with docker #20

Open inagaki-s opened 1 year ago

inagaki-s commented 1 year ago

I have a question about Docker. The following command was entered. "Workflow or tool uses unsupported feature:. Docker is required to run this tool: Command '['docker', 'images', '--no-trunc', '--all']' returned non-zero exit status 1." As a result, the following error message was output. "Workflow or tool uses unsupported feature: Docker is required to run this tool: Command '['docker', 'images', '--']'. Docker is required to run this tool: Command '['docker', 'images', '--no-trunc', '--all']' returned non-zero exit status 1." Docker Desktop is up and running behind Ubuntu. Up until now, Docker desktop was just up and running, with no particular changes made, and it was working fine. However, I would like to know what is the cause of this error this time.

docker_desktop
yyoshiaki commented 1 year ago

The error message "Workflow or tool uses unsupported feature: Docker is required to run this tool: Command '['docker', 'images', '--no-trunc', '--all']' returned non-zero exit status 1" indicates that the Docker command 'docker images --no-trunc --all' is failing for some reason.

This command is used to list all Docker images on your system, including intermediate images, and without truncating the output. If this command is failing, it could be due to a number of reasons:

  1. Docker Daemon Not Running: The Docker daemon might not be running or might be encountering an error. You can check if the Docker daemon is running by executing systemctl status docker or sudo service docker status.

  2. Insufficient Permissions: The user running the command might not have the necessary permissions to interact with the Docker daemon. If you're not running the command as root, you might need to add your user to the docker group. You can do this with the following command: sudo usermod -aG docker $USER, then log out and log back in.

  3. Corrupted Docker Installation or Images: There might be a problem with your Docker installation or with one of the Docker images on your system. You could try restarting the Docker daemon (systemctl restart docker or sudo service docker restart), or removing and reinstalling Docker.

  4. Docker Desktop Issues: Since you mentioned Docker Desktop, you might be running Docker inside a virtual machine or through some other layer of indirection. There might be issues related to this setup, such as networking problems or issues with the virtual machine.

inagaki-s commented 1 year ago

Thanks for getting back to me. I tried typing the two commands from answer 1: " sudo service docker status" and it outputs " * Docker is running". However, typing "systemctl restart docker" gives me "System has not been booted with systemd as init system (PID 1). Can't operate. Failed to connect to bus: Host is down". Why is this?