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treangenlab / Olivar

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
https://doi.org/10.1038/s41467-024-49957-9
GNU General Public License v3.0
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Primers missing from HTML file #19

Open DrownedMala opened 1 week ago

DrownedMala commented 1 week ago

Hello devs, as suggested in issue #13, I'm opening a new issue for the absence of graphical primers in the HTML output of olivar tiling. Here I attach the screenshots from my last generated primers (of today): full Full screen

partial_olivar Zoomed-in view: a primer should be seen starting at pos. 71

For reference, I used the olivar-validate python script with the snps module to build the variant file and ran olivar build with default settings, using the eukar db from NCBI as background. Anyway, even by other means (different tools than the olivar-validate), I still get no primers in the HTML file.

Let me know if I can give you any further helpful info. Cheers, Simone

edit: In addition, let me attach the HTML output of olivar-validate validate for the same case: versus

mxwang66 commented 1 week ago

@DrownedMala Thanks for opening this issue!

I did notice people might have different html outputs. Could you share your plotly version and your OS? And I assume you justed used the default parameters for Olivar?

DrownedMala commented 1 week ago

My plotly version is 5.24.1. OS is Ubuntu 20.04.6 LTS.

Yes, I did run it with default parameters, changing only temperature… But I've also tried leaving temperature as default, and it doesn't change the resulting HTML. By the way, previous versions of olivar did display the primers correctly.