[manualpipe] GISAID 20211129

[SamStudio8]

Brief description

• Error encountered in gisaid_uploader parse_fasta
• Additionally, error did not appear to propagate to Slack or cron email

Pipeline exit code: [Exit code]

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Executed by: [Name or initials] [Site code]

• [ ] I am sure this pipeline is not already running (Only relevant for non-flocked pipelines)

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• [ ] Engage pipeline via mqtt from a clean dedicated mqtt environment
• [ ] Disable NXF cache destruction (only applicable for ENA BAM pipe)
• [ ] Check output if necessary
• [ ] Check mqtt message is sent confirming completion, or send one if required (check in #tael-steam)
• [ ] Re-enable NXF cache destruction (if disabled)

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• [ ] Set appropriate issue flags and assignee

• [ ] Manual intervention complete

• "Normal" service disrupted? YES/NO

• If yes, describe impact:

[SamStudio8]

This was blocked by a bad sequence that made it through Elan, I am working with the supplier to have the sequence suppressed from the data set. It is already exluded from downstream analysis by Datapipe.

[SamStudio8]

Manually triggered GISAID 2021-12-02 with a 7 day lag (#14)