Terra CellRanger | Docker access permission denied

[Juliendly]

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 (2.0.2.strato) and docker options (i am a Broad member so gcr.io/broad-cumulus)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

[yihming]

Hi @Juliendly ,

Sorry for my late response!

Since you are within Broad, I would suggest you reaching out to Deeptha and use their bcl-convert workflow to cover the mkfastq step.

After that, you can then come back to our Cumulus Cellranger workflow with the generated FASTQ files as input, and run only the count step by setting run_mkfastq to false.

Sincerely,
Yiming

[Juliendly]

Hi Yiming, Thanks for your reply. I ended up being added to the Terra all_broad_users group and have been able to run the workflow since. As for the version, I haven't been able to run the 2.0.2.strato (but 2.0.2 worked well) since it looks like this version doesn't actually exist for the Docker image: [image: image.png] Thanks! Julien Le mar. 10 sept. 2024 à 16:29, Yiming Yang ***@***.***> a écrit :

…

Hi @Juliendly <https://github.com/Juliendly> , Sorry for my late response! Since you are within Broad, I would suggest you reaching out to Deeptha ***@***.***> and use their bcl-convert workflow to cover the mkfastq step. After that, you can then come back to our Cumulus Cellranger workflow with the generated FASTQ files as input, and run only the count step by setting run_mkfastq to false. Sincerely, Yiming — Reply to this email directly, view it on GitHub <#417 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQCRJG4D4FKQQIWXXYGCPRTZV5JDZAVCNFSM6AAAAABNEP3ZTKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBRHE2TINJUGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[yihming]

Hi @Juliendly ,

In this case, you may have to switch to Cellranger workflow v2.6.0, and set run_count to false. This should make the mkfastq step succeed.

[yihming]

After that, you can switch back to Cellranger workflow v2.6.3, set run_mkfastq to false, and use the generated FASTQ files as the input.

Sorry for this inconvenience, as our team doesn't have the permission to add or update docker images to gcr.io/broad-cumulus registry.