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Published 20 hours ago • verified publisher icon neherlab

localhost:800/my_species loads, I can view the Gene Cluster but no "Sequence Alignment" and no "Gene Tree"

Open NA1919 opened this issue 4 years ago • 5 comments

Hello,

I had panX some weeks ago and it was working perfectly, but I had to run tun the analysis again to add some new sequences. So with my new, larger dataset it does not work anymore. When I try to view my own data (as described with npm and localhost:800/), I see the Gene Cluster Table and the Strain Tree, But it does not let me chose and change anything. the sections "Sequence Alignment" and "Gene Tree" are always empty. When I view the TestSet, I can click on the items of the Gene Cluster Table but even if I click (and the line is marked/chosen), I cannot see any sequences. npm starts without any errors, although with this warning that I don't understand "WARNING in webpack: Using NoErrorsPlugin is deprecated. Use NoEmitOnErrorsPlugin instead." I don't see any other errors. When I try to view the old dataset -the one that had worked some weeks ago- I'm having the same issues.

Is there a way for me to figure out what might cause this problem? As far as I can tell, the analysis ran smoothly and the output seems fine.

Thank you in advance for any help :) Nurper

NA1919 avatar Feb 16 '21 16:02 NA1919

Hello,

I had the same problem as you. There seems to be no problem with my files.

Have you ever solved this problem? I can't find an answer to this question, so I'm inevitably leaving a reply.

thank you for your help. hj

hyoj-seo avatar Aug 17 '21 03:08 hyoj-seo

Hey, no this never worked out for me :( unfortunately I still have no idea why Good luck to you! :)

NA1919 avatar Oct 15 '21 16:10 NA1919

Same here guys. It's really annoying that everytime a nice tools is created, it is so poorly explained and not even maintained.. such a pity

Isoris avatar Jan 25 '23 09:01 Isoris

Hi Quentin @Isoris

I have written a little guide on how to run the tool currently:

https://github.com/neherlab/pan-genome-visualization/blob/master/README.md

There is also a neighbor branch where we discuss roughly the same:

https://github.com/neherlab/pan-genome-visualization/issues/16

Feel free to give it a try and let me know how it goes!

ivan-aksamentov avatar Feb 13 '23 14:02 ivan-aksamentov

Hello Ivan! Thank you so much for the information, I really appreciate your commitment. I will give it a look tomorrow morning. 😁 That's awesome! ~

Quentin.

Isoris avatar Feb 13 '23 19:02 Isoris