Auspice fails to fetch frequencies and frequencies cannot be normalized

Help and Getting Started
1

Hi,

I would love some support in getting the frequencies panel to work in Nextstrain. It would be great to add this feature to the Cambodian build we are currently developing here. Unfortunately I can’t get the frequencies panel to work both in my build and in the “getting started” tutorial build.

To my understanding the only requirements to enable the panel are:
1/ Adding “frequencies” to the panels in the auspice JSON. Which I have done.

"
“panels”: [
“tree”,
“map”,
“entropy”,
“frequencies”
],
"

2/ Making sure a “tip-frequencies” JSON is available for auspice to fetch. Which is the case

Augur doesn’t report any errors. However when I visualize the auspice JSON the tool prompts an error “Failed to fetch frequencies” and the Frequencies tab indicates “Frequencies cannot be normalized”.

You can see an example of this here: auspice

I have been troubleshooting for a while now and have been unable to find a fix. All help more than welcome!

Cheers,

Koen

2

Hello,

Community urls are good practice for discussion.nextstrain.org as I could immediately see in ncov-Cambodia-build/auspice at main · Koen-vdl/ncov-Cambodia-build · GitHub that you need to rename ncov-Cambodia-build_4m_global_tip-frequencies.json as ncov-Cambodia-build_4m_tip-frequencies.json

2 Likes
3

Thank you so much for solving this babarlelephant. I indeed messed up the naming convention of the json files! derp

4

Hey similar issue I am facing I want to see normalize frequencies for my .json file. but says frequency can not be normalized.
If sequence number would be imitatiations can you please tell me how many sequences are required to get the normalized frequency and I have 210 sequences in it.

also, When I try to visualize tip-frequencies.json file it shows error of file can not read.

Let me know solution for this
Thanks in advance

5

Hi @pratibha - Could you provide more context here? Is the dataset public?

6

No. I have prepared my own dataset.