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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
GNU General Public License v3.0
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HTML Report Figure's Aren't Showing #49

Closed Mrromeros closed 2 years ago

Mrromeros commented 2 years ago

Hello, I used Nanovar on a test dataset of MinION data from SRA, and was able to produce the .pass.vcf and .total.vcf files without any issues, and the HTML report is generated but I cannot view any of the figures.

I have attached the image below of what my report looks like. I am not sure if this is just a problem with the HTML or the actual execution, seeing how the program executed without errors, I don't see why it wouldn't populate the graphs.

For context, I am currently running NanoVar v1.4.1 through Conda (Python=3.8) on Ubuntu 20.04.

NanoSV_problems

cytham commented 2 years ago

@Mrromeros The HTML should only be opened in the folder it was created as it is not a standalone file. Did you take it out of the original folder? Sorry for this inconvenience

Mrromeros commented 2 years ago

Yes, I copied just the HTML from wsl mounted drive to my main drive so I could open it easier, since I am not sure how to open an HTML file in ubuntu. However, even when I copy over all the other 2 vcf files to the same folder my graphs don't show any figures. Is there some other dependency I am missing? Or can I only open it in the direct output folder?

cytham commented 2 years ago

The HTML file requires the fig, css and js folders, so please transfer them too and make sure they are in the same folder.

Mrromeros commented 2 years ago

That solved the problem! Thank you for the quick assistance!