query vs target?

[evo-eco-gen]

The instructions explain the parameters as follows:
"Query A fasta file containing the target sequences
Reference A fasta file containing the query sequences"

Is it not the other way around?

[AntoineHo]

Hello,

Indeed, this is an error in the "help" message.

The "Query" should be a fasta file with the same sequence identifiers as found in the first column of the .paf file and Reference should be a fasta file with sequence identifiers found in the 6th column of the .paf file.