epicov: empty tips on time-scaled tree

PoonLab / covizu

Rapid analysis and visualization of coronavirus genome variation

https://filogeneti.ca/CoVizu/

MIT License

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epicov: empty tips on time-scaled tree #478

Closed ArtPoon closed 1 year ago

ArtPoon commented 1 year ago

There are bunch of rect elements with width="NaN" and cidx="cidx-undefined"

GopiGugan commented 1 year ago

clusters.json did not get updated in the last run. Similar issue to #464. Commit ba709c4 should have fixed the issue.

Looking into why convert_json failed. Temporarily replacing the epicov data files with the ones from the last successful run (April 21)

GopiGugan commented 1 year ago

convert_json ran without issues. Looks like the batch.py script terminated earlier. A temporary file with the output from convert_json was created but failed to transfer over to the web server:

https://github.com/PoonLab/covizu/blob/7cf87ca2a882490cc93fb7144cd429e691e9fab9/batch.py#L207-L213

ArtPoon commented 1 year ago

This is related to an OOM error - need to upgrade RAM on head node or launch main process on one of the newer compute nodes

ArtPoon commented 1 year ago

Temporary fix is to run the backend on Paphlagon until I can come in to upgrade the RAM on BEVi head node