Re: workflow error

[Yuan Lian]

On Mon, Apr 8, 2024 at 2:02 PM Yuan Lian <yl...@broadinstitute.org> wrote:

Hi there,

I'm Ansel from Broad Institute and we're trying the 2nd step analysis with cumulus-AC_1c/Cellranger_aggr:branch_from_tag_2.5.0, but I keep getting this error below, the error saying I should specify backend  which i tried gcp and gcs but it looks like the variable was not passing to the script. So I'm wondering if there are any other parameters that I should change?

Thanks for your help!

Ansel

Attach the input I used for the workflow: 

{"cellranger_aggr.normalize":"none","cellranger_aggr.preemptible":"${2}","cellranger_aggr.backend":"${}","cellranger_aggr.secondary":"${true}","cellranger_aggr.input_counts_directories":"gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/117990_1,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/117990_2,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/117992_1,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/8_125110_1LR,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/7_118284_1LR,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/9_118487_2LR,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/sciatic_11_12,gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/sciatic_9_10","cellranger_aggr.output_directory":"gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/aggr","cellranger_aggr.aggr_id":"sciatic_sample"}

filenames [filenames ...] strato cp: error: the following arguments are required: --backend Traceback (most recent call last): File "<stdin>", line 21, in <module> strato cp -m -r gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/117990_1 /cromwell_root File "/usr/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['strato', 'cp', '-m', '-r', 'gs://fc-89ec6b61-9eaf-4b5a-9c85-a160299e8d94/output/117990_1', '/cromwell_root']' returned non-zero exit status 2.

[Yiming Yang]

Hi Ansel,

May I know which workflow you are using? There is no "Cellranger_aggr" workflow in our repo. Is it in your repo which is built on top of our workflow? If so, could you point which?

This issue is because the workflow uses a docker image which has an older version of Stratocumulus installed. This older version requires "--backend" option, while we remove it in later versions. So I need to know which docker image your workflow uses, so that I could rebuild it with the later version of Stratocumulus.

Sincerely,

Yiming

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γνῶθι σεαυτόν.

[Yiming Yang]

Hi Ansel,

Your workflow uses our docker image "quay.io/cumulus/cellranger:7.1.0", which does use an older version of Stratocumulus. I've updated the docker image. Please try it again, and let me know if the issue persists.

Sincerely,

Yiming

On Tue, Apr 9, 2024 at 7:00 AM Yuan Lian <yl...@broadinstitute.org> wrote:

Hi Yiming,

Here's the link to the workflow I use: https://dockstore.org/workflows/github.com/abhiachoudhary/cumulus-AC_1c/Cellranger_aggr:branch_from_tag_2.5.0?tab=info,

It might built from your original workflow.

Thank you!

Ansel 

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γνῶθι σεαυτόν.

[Yuan Lian]

Thank you for your help Yiming! It works now.

Best,

Ansel