Ipyrad de novo for variant calling

Question

[giulia.trauzzi]

Hello everyone,

I am trying to run ipyrad to generate a SNP data set de novo (I do not have a good enough reference genome for my species). I have already demultiplexed my raw data and removed the barcodes and adapters. Does anyone have an example of what the params file should look like to only do the variant calling with ipyrad? What is more when I try to run the script, this is the error message I get

ipyrad.assemble.utils.IPyradError: Could not find saved Assembly file (.json) in expected location. Checks in: [project_dir]/[assembly_name].json Checked: /nfs/scratch2/trauzzgi/./ipyrad_caller/output/.json

Can anyone help me understand what this means?

Many thanks

Giulia

[Betsy]

Were you ever able to resolve this error? I am having the exact same problem trying to run ipyrad on already demultiplexed fq.gz files

[giulia.trauzzi]

I ended up using STACKS de novo. I never solved the issue, unfortunately.

Answer 1

[Abieskawa]

Ohh, I think use should run the the first step, I encounter similar problem with you last week.