COG-UK Docs

View the Project on GitHub COG-UK/docs

Updated 2021-03-03 by @samstudio8

When is metadata and sequence data processed on CLIMB?

Timeline

Inbound pipeline

The inbound distribution pipeline (called Elan) currently runs every day (including weekends). The dataset as it stands after the Friday pipeline is used for weekly reporting. The pipeline currently consists of the following events:

Time Event Descirption
1605 End of day check 1 Using the uploaded metadata, Majora generates a list of samples to check against the file system.
1630 End of day message 1 The Majora bot annouces in #inbound-distribution the number of new sequences for each site that can be linked to metadata. It will also list the number of sequences that appear to be missing uploaded metadata, or metadata that appears to be missing uploaded sequence.
1705 End of day check 2 Using the uploaded metadata, Majora generates a list of samples to check against the file system.
1730 End of day message 2 The Majora bot announces in #inbound-distribution the number of sequences pulled for each site, the week’s total and the new cumulative upload total.
+1 day 0501 Permissions check A cron job runs chmod to ensure all the upload directories are readable by the pipeline.
+1 day 0505 Pre-pull Using the uploaded metadata, Majora generates a list of samples to check against the file system.
+1 day 0601 Pipeline starts If nothing horrible has gone wrong, the pipeline will start.
~ Pipeline ends After a few hours, the Majora bot will annouce to #inbound-distribution the number of sequences that made it through the pipeline and passed basic QC.

How long does the pipeline take?

Elan can process approximately 1000 samples an hour on a good day. Combined with around 90 minutes for “post-Elan publishing”, an average pipeline of 3000 samples should take around 5 hours to complete (ready for lunch). For PHA subscribed to Asklepian, processing time on a good day is around 90 minutes (mid afternoon).

Outbound pipeline

GISAID and ENA pipelines run on Mondays. All sites are automatically enrolled for ENA uploads. You must however opt-in for GISAID uploads. Data uploaded over the weekend will miss the official reporting cut-off, but will be included in Monday’s outbound pipeline.

Note


Published 2020-05-29. Updated 2021-03-03. Page maintainer @samstudio8.