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HumanCellAtlas / secondary-analysis

Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform
https://pipelines.data.humancellatlas.org/ui/
BSD 3-Clause "New" or "Revised" License
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Analyze scRNAseqSystemicComparison dataset #843

Closed kbergin closed 4 years ago

kbergin commented 4 years ago

Analyze the "Systematic comparative analysis of single cell RNA-sequencing methods" dataset (project id: 88ec040b-8705-4f77-8f41-f81e57632f7d) which is a combination of 10x v2 and SS2 data (both human and mouse)

We ran analysis for all of the human samples: https://job-manager.caas-prod.broadinstitute.org/jobs?q=project_shortname%3DscRNAseqSystemicComparison

There's a github issue to analyze the mouse data after SS2 mouse support is available in production: https://github.com/HumanCellAtlas/secondary-analysis/issues/817

┆Issue is synchronized with this Jira Story

kbergin commented 4 years ago

➤ Saman Ehsan commented:

The 3 failed workflows for SS2 human data are re-running here: https://job-manager.caas-prod.broadinstitute.org/jobs?q=project_shortname%3DscRNAseqSystemicComparison%26status%3DRunning ( https://job-manager.caas-prod.broadinstitute.org/jobs?q=project_shortname%3DscRNAseqSystemicComparison%26status%3DRunning )

kbergin commented 4 years ago

➤ Saman Ehsan commented:

Mouse bundles can be analyzed after the next prod promotion

kbergin commented 4 years ago

➤ Saman Ehsan commented:

Optimus analysis is complete for the 3 human data bundles, and is running for the 2 mouse bundles: https://job-manager.caas-prod.broadinstitute.org/jobs?q=project_uuid%3D88ec040b-8705-4f77-8f41-f81e57632f7d%26name%3DAdapterOptimus ( https://job-manager.caas-prod.broadinstitute.org/jobs?q=project_uuid%3D88ec040b-8705-4f77-8f41-f81e57632f7d%26name%3DAdapterOptimus )

kbergin commented 4 years ago

➤ Saman Ehsan commented:

SmartSeq2 analysis is complete! There is one Optimus workflow that is having problems with the SplitBambyCellBarcode step: https://job-manager.caas-prod.broadinstitute.org/jobs/9bed3cd3-d0a5-4b58-bfaa-7471ac40c81c?q=project_uuid%3D88ec040b-8705-4f77-8f41-f81e57632f7d ( https://job-manager.caas-prod.broadinstitute.org/jobs/9bed3cd3-d0a5-4b58-bfaa-7471ac40c81c?q=project_uuid%3D88ec040b-8705-4f77-8f41-f81e57632f7d )

VM logs: https://console.cloud.google.com/compute/instancesDetail/zones/us-central1-b/instances/google-pipelines-worker-d034f115e9eb4fe821ae239839578bd0/console?project=hca-dcp-pipelines-prod&authuser=0&folder&organizationId=215427897968#end ( https://console.cloud.google.com/compute/instancesDetail/zones/us-central1-b/instances/google-pipelines-worker-d034f115e9eb4fe821ae239839578bd0/console?project=hca-dcp-pipelines-prod&authuser=0&folder&organizationId=215427897968#end )

kbergin commented 4 years ago

➤ Chengchen Wang commented:

I retried the last workflow without doing anything but it succeeded: https://job-manager.caas-prod.broadinstitute.org/jobs/8f453448-6536-4195-bf58-051954f055a0 ( https://job-manager.caas-prod.broadinstitute.org/jobs/8f453448-6536-4195-bf58-051954f055a0 )

I suspect it’s because the recent update of CaaS which fixed and issue that stops caas from performing memory-retryfeature.