Hi @matoro,
Thanks for posting! I am a little unclear on your question — are you trying to compute alpha rarefaction plots with multiple metrics at once? Or are you trying to use a QIIME1 text file as input? I assume the former, based on the title.
To compute multiple metrics, you need to pass the metrics parameter multiple times if you want to use metrics other than the default. E.g., --p-metrics X --p-metrics Y --p-metrics Z
Please let me know if that solves your question!