I was trying to run the “Moving Pictures” tutorial on VirtualBox. After the downloading steps, I tried to get the .qza file following the tutorial using:
qiime tools import
–type EMPSingleEndSequences
–input-path emp-single-end-sequences
–output-path emp-single-end-sequences.qza
However, it falied and I get the error message:
bash: qiime: command not found
Then I retried the “–output-path emp-single-end-sequences.qza” command, and I get another error message:
bash: --output-path: command not found
How would I fix this?
Welcome to the forum, @MAJAIN!
Please confirm your virtualbox image has successfully installed qiime 2. You can do this by opening the Virtualbox, opening a terminal window, and entering
qiime info
Please paste your results here. (There are good directions for setting up copy-paste in this tutorial) The ‘preformatted text’ option in the menu bar will help keep your post readable.
NOTE also: --output-path ...
is an argument to qiime tools import
, not an command per se, and cannot be used independently of qiime tools import
and its other required arguments. Careful attention to punctuation (e.g. --
, not -
at the beginning of arguments, and backslashes to break long commands across multiple lines) might also help you get you on the right track.
Happy qiime-ing!
Chris
Hi @ ChrisKeefe!
Thanks for your reply, and it really helps! I tried “qiime info” as you mentioned, and finally figured out that the error occured because I was trying to solve the data through root access:sweat_smile: Everything works properly now, thanks for your advice.
MAJIAN
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