@isaacovercast Thank you so much for your prompt reply. I'm running two datasets, both with the same parameters. Datatype is paird3rad (EcoRI and claI). I used the default parameters except for the max_barcode_mismatch (=1) and the filter adapters (=2). In one dataset, I got an error that one sample is missing (I will run step 6 again), but the other one just says error in filter_stacks on chunk 0.