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Troubleshooting with containers

When working with containers, there are multiple potential sources of problems:

  1. Interacting with the Genomics England HPC
  2. Singularity
  3. The container
  4. The software within the container

Tracing the source of the error may require cross-referencing between the documentation for all these sources. Here, we will point you towards where you might look for information about different types of errors.

FATAL error on pull, Unable to get library client

When trying to pull a container, I received an error:

FATAL: Unable to get library client configuration: unable to get library service URI: error making request to server:

 You need to modify the path to the container to include the artifactory re-routing.

Genomics England use artifactory re-routing to allow containers to be pulled into the RE, but not be pushed out.

FATAL error on pull, failed to get manifest

When trying to pull a container, I received an error:

FATAL: While pulling image from oci registry: error fetching image to cache: failed to get manifest for quay.io/nonexistent/repo

 Singularity cannot find a container with that name in the repository. Check that you have spelled the path correctly and that the container is not private.

FATAL error on exec

When trying to execute a container, I received an error:

FATAL: While checking image: could not open image /path/to/your/working/folder/container.sif: failed to retrieve path for /path/to/your/working/folder/container.sif: lstat /path/to/your/working/folder/container.sif: no such file or directory

 Singularity cannot find a container with that name. Check that you have pulled it correctly, and that you have spelled the path and filename correctly in your exec command.