option for reference sequence

[wbsimey]

I have tried many different ways to load the reference fasta file, but no luck. I tried no flag and get unrecognized command, I tried 'target' or 'reference' and get unrecognized command, I tried --target, I do not see any other flag to load the reference. I searched the help file and there is no 'reference' in the options. Please add some example commands. Thank you.

[abacigalupo]

Same was happening to me but I had an error ... the -p was not separated by a space from the previous information. This may be happening to you as well. Not necessarily in the same place. After solving that, it recognized both target and reference sequence just by their position (no need to write "target" or "reference"). Below is an example; it also worked with the whole path for each of the files.
e.g liftoff ... -p 50 seq1.fasta seq2.fasta
I hope that helps.