Error running SpaceRanger Workflow from lilab-bcb/cumulus
After inserting the inputs for samplesheet and outputs in the format "gs://...", backend as "gcp", memory as "120G", num_cpu as 32, run_count as true, run_mkfastq as false (my files are fastq), secondary as true, spaceranger_version as "2.0.0" or other I receive failure with the following message "job spaceranger_workflow.generate_count_config:NA:1 exited with return code 1 which has not been declared as a valid return code". Does anyone know how to help?
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3 comments
Hi Rômulo,
Thank you for writing in about this issue. Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
Please provide us with
We’ll be happy to take a closer look as soon as we can!
Kind regards,
Pamela
Workflow link:
Lung Einstein - Dashboard (terra.bio)
Submission ID:
d0407352-ddcd-412d-ae0d-0cfe2c246168
Submission Link:
https://console.cloud.google.com/storage/browser/fc-05ff183a-e254-4336-8f11-54b553be94d1/submissions/d0407352-ddcd-412d-ae0d-0cfe2c246168?authuser=ayzrael@gmail.com
Workflow ID:
264c10fe-80ba-4c2a-871a-fcb847c013ab
Thank you in advance
Hi Romulo,
Thank you for providing that. When looking at the backend log for the failed workflow, it looks like the workflow is failing with the following error that indicates an issue with the "Flowcell" column of your input CSV.
In your input CSV, it looks like you just have the same link to the main workspace bucket path for each sample in the "Flowcell" column. From the SpaceRanger documentation, it looks like this column should contain different Google bucket URLs for BCL folders.
Please let me know if this information is helpful.
Kind regards,
Pamela
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