I have been trying to run a script on my terminal and unfortunately when i do i do not understand the resopnse the terminal gives. I've provided the script and response below; (">> " is my PS1)

>> ./metaphlan2.py --input_type fastq

BowTie2 output file detected: stdin_map.bowtie2out.txt

Please use it as input or remove it if you want to re-perform the BowTie2 run.

Exiting..

please explain what it is requesting me to do, and if you are so kind, to provide a script that might point me in in the right direction, thank you!