@isaacovercast Thank you very much! The way that worked for me was to create a folder for each of my individual pools and run step 1 on each one of them separately since they have the same inline barcodes. Then, I created another ipyrad folder to run the analysis starting with the demultiplexed files that were generated for each of my pools in the step 1 run. I copied all the demultiplexed files from each pool in a folder that I pointed in the sorted_fastq_path parameter. That worked great! Another possibility I thought was merging the runs before step 2 using "ipyrad -m", but I didn't quite understand how I would set this up from the help. Anyway, it worked without the need of merging in ipyrad.