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PoonLab / covizu

Rapid analysis and visualization of coronavirus genome variation
https://filogeneti.ca/CoVizu/
MIT License
45 stars 20 forks source link

Error generating epicov data #523

Closed GopiGugan closed 2 months ago

GopiGugan commented 4 months ago 
[covizu@BEVi ~]$ tail batch.log
...
🏄 [12:20:25.736335] start BQ.1.1, 73245 entries
🏄 [12:27:05.707608] Parsing output files
Failed to retrieve metadata for accession EPI_ISL_18554387

https://github.com/PoonLab/covizu/blob/12a9d08b70d754a30b72d84636affb28d3934765/covizu/utils/gisaid_utils.py#L327-L341

ArtPoon commented 4 months ago

Can we grep for this accession number in that provision file?

GopiGugan commented 3 months ago

This accession number existed in a previous provision file, but not in the latest file. Investigating how this accession number is showing up in the current clusters.json file

ArtPoon commented 3 months ago

Sometimes sequences are retracted in the database so the record that appeared in a previous provision file would no longer appear in subsequent files.

GopiGugan commented 3 months ago

https://github.com/PoonLab/covizu/blob/22f4f4cac124292e1f404c83f7068c3e4033fd55/batch.py#L320-L338