Zika Index Sequences Error


I finished completing the installation steps and completed the Zika tutorial. However, when I moved onto the next step to create a workflow, I got an error in the “Index Sequences” step. I used the exact code, but got the error below. Do you know what went wrong?
zika code error

Hi @mtcaton, sorry to hear you’re running into issues again.

This error is because most of our docs are written for Linux/macOS system shells in mind. While some code blocks might also work in PowerShell, there are a few such as this one which require some modifications to work in PowerShell. In this case, the \ is a shell line continuation character that needs to be replaced by `. So your command should look like this:

augur index `
  --sequences data/sequences.fasta `
  --output results/sequence_index.tsv

Most of our Windows users use WSL, but clearly we should have better documentation for PowerShell users like you. I’m not sure when we’ll get around to it, but in the meantime we’ll try our best to resolve your issues here.

– Victor