How to remove primer and index from demux.qza

Hi @Rishikesh12,

Basically what this error is saying is that your input for qiime cutadapt demux-paired is already demultiplexed. You need to input multiplexed data into qiime cutadapt demux-paired so that the command can demultiplex your data.
I can see two ways this possibly happened. However I am not sure exactly what steps you took given the information you provided.

  1. You imported already demultiplexed data. If this happened you would probably not have barcodes in your sequences and you would just skip the qiime cutadapt demux-paired command.
  2. You imported multiplexed sequences and then you ran a command that demultipexed your sequence. Then you used cutadapt trim-paired and now you are trying to demultiplex again.
    If this is the case, I would highly suggest that you re-read the Demultiplexing and Trimming Adapters from Reads with q2-cutadapt tutorial that I linked above and here. These steps need to be followed in a specific order or else the types of inputs are going to be wrong like you see in the error message you sent.

In order to help you more on this, I would need to know all the commands that you ran to get to this error. Please list all of them in your next reply.

Hope this helps!

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