QIIME cannot run python script

Question

[pzh817]

I cannot run python script in QIIME 2.

I downloaded QIIME2 (https://data.qiime2.org/distro/core/2018.4), unzipped the downloaded folder in Windows 7, and then installed QIIME 2 in VirtualBox (Version 5.2.12). Then I tried to run a command, summarize_taxa.py. I got this error message "bash: summarize_taxa.py: command not found.

Is there anybody who can help? Many thanks.

[Joe]

You tried to run a python script with bash.

[steve]

try running python summarize_taxa.py, from the directory where summarize_taxa.py is located

[jeremieaauger]

I have been trying to locate these scripts for a little while! I have qiime2 installed and fully working on my laptop, but can't seem to find them! Are they downloaded by default? I don't see any repo that has them! summarize_taxa.py; pick_otus.py; make_3d_plots.py; etc.) Thanks! -JA

Answer 1

[al-ash]

No such scripts are part of QIIME 2: these are only in QIIME.