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?