Importing Data and Running Initial MetaPhlAn


I just downloaded MetaPhlAn 3.0 and I am a new user. I work with a collaborator who shared data with us via Qiita. I am used to using qiime2 on windows subsytem linux (ubuntu). However I am not super familiar with the language used in your github tutorial - specifically the formatting for running metaphlan (metaphlan3 · biobakery/biobakery Wiki · GitHub).

I am struggling to import all of my data into my created directory due to the nature of the data shared with me via my collaborator. I have raw fast.q files that are all GZ files, but because there are so many when I download them they are in a zipped file. So I a still importing those into my folder with wget and a link from my data but in the meantime I used “explorer.exe .” and pasted just one of the fastq.gz files into the folder to run a test.

I am running into this issue “UnboundLocalError: local variable ‘ls_f’ referenced before assignment”.

Images of my code:

Any feedback on this issue or the code I am running would be greatly appreciated.

Thank you,

Hi @nagr4657
Could you specify the exact metaphlan version you are running? You can check it with metaphlan --version

I am using version 3.0.

Hi @nagr4657
I would try to update metaphlan 3.0 to the latest version available 3.0.14 that should solve this problem