Investigate RunEmptyDrops error in HumanColonicMesenchymeIBD HCA dataset - Githubissues

HumanCellAtlas / secondary-analysis

Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform

https://pipelines.data.humancellatlas.org/ui/

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Investigate RunEmptyDrops error in HumanColonicMesenchymeIBD HCA dataset #634

Closed kbergin closed 5 years ago

kbergin commented 5 years ago

Several workflows in the HumanColonicMesenchymeIBD dataset in production are failing due to errors in the RunEmptyDrops task. Investigate whether this is an issue with the input data and/or the task itself.

https://job-manager.caas-prod.broadinstitute.org/jobs/c4734904-70c9-4297-bcb8-ac0f6749609c?q=workflow-version%3Doptimus_v1.3.2%26project_shortname%3DHumanColonicMesenchymeIBD%26status%3DFailed Error: an error occured while running emptyDrops\! {{Error: need at least four unique 'x' values }}

https://job-manager.caas-prod.broadinstitute.org/jobs/5de6c285-2a4e-4dcf-afd4-20a615f0c1e8?q=workflow-version%3Doptimus_v1.3.2%26project_shortname%3DHumanColonicMesenchymeIBD%26status%3DFailed

Error: an error occured while running emptyDrops\!

Error: insufficient unique points for computing knee/inflection points

Link to all workflow failures for this dataset for reference: https://job-manager.caas-prod.broadinstitute.org/jobs?q=workflow-version%3Doptimus_v1.3.2%26project_shortname%3DHumanColonicMesenchymeIBD%26status%3DFailed

AC:

If it’s an error with emptyDrops, file a bug report with the tool creators and don’t process the samples
If it’s an issue with the data, don’t process those samples
If it’s an issue with our pipeline, fix or make a ticket to fix.

┆Issue is synchronized with this Jira Ops Needs

kbergin commented 5 years ago

➤ Saman Ehsan commented:

We can close this since this data wasn’t run with the correct pipeline – my mistake!