Terra CellRanger | Docker access permission denied

[Julien Dilly]

Dear Cumulus Team,

I am trying to run the Cellranger-arc-mfastq and Cellranger-arc-count workflow (github.com/lilab-bcb/cumulus/Cellranger:2.6.3) in Terra with default versions and docker options and it appears that I do not have access to the dockers, with the following error being outputted:

Task cellranger_arc_mkfastq.run_cellranger_arc_mkfastq:NA:1 failed. The job was stopped before the command finished. PAPI error code 7. Execution failed: generic::permission_denied: pulling image: docker pull: running ["docker" "pull" "gcr.io/broad-cumulus/cellranger-arc:2.0.2"]: exit status 1 (standard error: "Error response from daemon: pull access denied for gcr.io/broad-cumulus/cellranger-arc, repository does not exist or may require 'docker login': denied: Permission denied for "2.0.2" from request "/v2/broad-cumulus/cellranger-arc/manifests/2.0.2".\n")

Would you be able to indicate if there is a specific process to get access to it?

Thank you,
Julien

[David Lieb]

Hi Julien,

I got that exact error last year when running another Cumulus workflow and was able to resolve it by contacting Terra Support:

Hi David,

 

Thanks again for writing in! This docker image actually requires that your Terra account is part of the all_broad_users group in Terra which is probably why you're getting the permissions issue. I just added you (dl...@broadinstitute.org) to this group. Please let me know if you are still experiencing the error!

 

Kind regards,

Pamela

However, my account uses a Broad email address. So not sure if the same solution would work for you.

David

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[Julien Dilly]

Thank you David!

I also thought that this issue was due to me not being added to the all_broad_users group but after being added I am still experiencing the same issue.

Julien

[Alexis Caulier]

Hello Julien,

I also get the same error: 

Task cellranger_arc_mkfastq.run_cellranger_arc_mkfastq:NA:1 failed. The job was stopped before the command finished. PAPI error code 9. Execution failed: generic::failed_precondition: pulling image: docker pull: running ["docker" "pull" "gcr.io/broad-cumulus/cellranger-arc:2.0.2.strato"]: exit status 1 (standard error: "Error response from daemon: manifest for gcr.io/broad-cumulus/cellranger-arc:2.0.2.strato not found: manifest unknown: Failed to fetch \"2.0.2.strato\" from request \"/v2/broad-cumulus/cellranger-arc/manifests/2.0.2.strato\".\n")
Were you able to troubleshoot it?

Thank you,

Alexis

[Yiming Yang]

Just include Deeptha from Broad into this email thread.

Hi Deeptha,

As you can read from the quoted email content below, there are still Broad users using Cumulus Cellranger workflow for running the mkfastq step. Since our team has lost the access to modify/update docker images in gcr.io/broad-cumulus repo, I just wonder how to handle such a kind of user support cases in the future. 

I have 2 options in mind:

1. I update the docker images, and then ask you to update accordingly by pulling them into gcr.io/broad-cumulus registry.
2. I direct users to you, and you will guide them to use your bcl-converter workflow to cover the mkfastq step. After that, users can come back to use Cumulus Cellranger workflow with the generated FASTQ files as input, and set "run_mkfastq" to false when running the count step.

What do you think?

Sincerely,

Yiming

To view this discussion on the web visit https://groups.google.com/d/msgid/cumulus-support/6f4e336b-f92e-49c7-98a8-2072326ae108n%40googlegroups.com.

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