Narrative making

Help and Getting Started
1

I did Covid analysis by following the nextstrain tutorial and successfully created auspice based visualization “Result.json” file. I can open and check the same in my localhost.

I want to make narrative as described in tutorial but not understand properly.

I make a “narrative.md” file which look like this

title:Covid Analysis
author: “ME”
Year:“2021”
dataset:“http://localhost:4000/Covid?d=tree”
abstract:“This is Covid Ananlysis Result”

then I ran
auspice view --datasetDir dataset/ --narrativeDir narratives/
the error is “Failed to read Covid_root-sequnec.json”
what I am missing?
however
auspice view --datasetDir dataset/

running perfect on my localhot

2

Hi @avrajit - thanks for reaching out, I think we can solve this with a few more details from you.

  • What is currently happening when you load your narrative? If you have this stored at narratives/narrative.md then you should be able to load http://localhost/narrative. Could you post any console errors / terminal messages to help us here?
  • The message of “Failed to read Covid_root-sequence.json” is inconsequential in this situation.
  • What dataset do you wish to visualise? You indicate you’re dataset is dataset/Result.json but the URL in your narrative (http://localhost:4000/Covid) will be using dataset/Covid.json.
  • In your narrative.md you’ll need at least a paragraph of content (currently you only have the frontmatter). Here’s an example:
---
title:Covid Analysis
author: “ME”
Year:“2021”
dataset:“http://localhost:4000/Covid?d=tree”
abstract:“This is Covid Analysis Result”
---

# [Slide 1](http://localhost:4000/Covid?d=tree)

Slide 1 text
3

Hi James,
Thanks for your response. here is my terminal output

(nextstrain) @desktop:~/Project_Details/Mycovid/Covid_result_Nextstrain$ auspice view --datasetDir auspice/ --narrativeDir narratives/


---------------------------------------------------
Auspice server now running at http://localhost:4000
Serving auspice version 2.29.1
Looking for datasets in /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/auspice
Looking for narratives in /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/narratives
---------------------------------------------------


GET AVAILABLE returning locally available datasets & narratives
trying to access & parse local narrative file: /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/narratives/covidNarrative.md
GET AVAILABLE returning locally available datasets & narratives
GET DATASET query received: prefix=/Covid
GET AVAILABLE returning locally available datasets & narratives
GET DATASET query received: prefix=/Covid&type=root-sequence
[warning]	Failed to read /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/auspice/Covid_root-sequence.json
trying to access & parse local narrative file: /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/narratives/covidNarrative.md
GET AVAILABLE returning locally available datasets & narratives
trying to access & parse local narrative file: /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/narratives/covidNarrative.md
GET AVAILABLE returning locally available datasets & narratives
trying to access & parse local narrative file: /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/narratives/covidNarrative.md
GET AVAILABLE returning locally available datasets & narratives
trying to access & parse local narrative file: /home/avc/Project_Details/Mycovid/Covid_result_Nextstrain/narratives/covidNarrative.md
GET AVAILABLE returning locally available datasets & narrative

I understand your point. But I am following this tutorial Writing a Narrative — Nextstrain documentation

which is instructing add the local host address where your auspice result is running.

Is there any tutorial how to make narrative for nextstrain auspice result? please share

4

It looks like you’ve written a narrative narratives/covidNarrative.md – what happens when you load that narrative in your locally running auspice? I’m not sure what is not working from your messages. The tutorial you linked to is the best example to follow currently.

5

in my terminal

the error is

verbose] Error: ENOENT: no such file or directory, open ‘/home/avc/Covid_result_Nextstrain/auspice/Covid_root-sequence.json’

What this mean? what is root-sequence.json?

6

It’s an optional sidecar file containing the root sequence, here’s how you can create it. It’s optional and shouldn’t matter for your narrative unless you want to colour the tree on a sequence position without any mutations (i.e. all sequences share the same base).

7

Thanks for explanation. Is there any way I can share my auspice file with you. Is that possible?

8

Sure thing - the easiest is probably through nextstrain community sharing. We would be happy to add it to nextstrain.org/sars-cov-2 as well, if you’d like.