Hi @jakub.zarsky! In the future, it would be really helpful if you provide the full command you are running - this helps contextualize the error message you are reporting! With that in mind, I suspect this is a bug related to how cutadapt saves data vs how QIIME 2 expects to see it. Would you be able to provide your data, and the exact command you ran to me? A link to download the files from something like Dropbox or Google Drive would be perfect (you can send in a direct message to me if privacy is a concern). This will help us reproduce the issue, and come up with a gameplan for fixing it. Thanks! 