Workflow error- Cellranger count

[Francesco Corrado]

Hi all,
I am trying to run Cellranger count on a single sample using the Cellranger workflow v2.6.2 in Terra.
I am using Cellranger V6.0.1 and reference GRCh38-2020-A.
I followed the instruction at https://cumulus.readthedocs.io/en/stable/cellranger/index.html#sample-sheet to preprare sample sheet, input and output folders.

When I run the workflow,I get the following failure message: "Job cellranger_count.run_cellranger_count:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
When I open the log file I see the following error=FileNotFoundError: [Errno 2] No such file or directory: 'strato': 'strato'
Thanks so much in advance for any assistance!

Edit: Using Cellranger V8.0.0 solved the issue in workflow v2.6.1 but I still need to use cellranger v6.0.1

Francesco

[Yiming Yang]

Hi Francesco,

Thanks for reaching out. I've updated the cellranger v6.0.1 docker image to include the new packages. Please try it again and let me know if the issue persists.

Sincerely,

Yiming

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γνῶθι σεαυτόν.

[Francesco Corrado]

Hi Yiming thank you so much for your support!! Now it is working, I will let you know if I have other errors.

Again, many thanks for the help.

Best,

Francesco