I have been trying to run a script on my terminal and unfortunately when i do i

Question

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!

Explanation / Answer

Solution: - First of all in a python terminal. The script can't be run like a bash terminal.

There are different method or python syntax is there to run a python script within python prompt.

>> ./metaphlan2.py will not perform here.

Instead you want to run your phython script

>>>execfile('metaphlan2.py') for python 2.0 and above.

OR

>>>exec((open("metaphlan2.py").read()) for python3 and above.

You can even use another method,

>>>import os

>>>os.system('./metaphlan2.py')

This will also work correctly.

>>>import subprocess

>>> subprocess.check_output(['./metaphlan2.py'], shell=True)

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