Problems with Converting to .qza

Hi everyone! Sorry to bother you. I am new to QIIME 2 and to the world of bioinformatics. I have been stuck on something for days and need help with the following:
Aquí tienes la traducción al inglés:

I am following the program tutorial and the problem arises when I want to convert the files to QZA format. Everything was fine until then. But when I paste this command:

qiime tools import
--type EMPSingleEndSequences
--input-path emp-single-end-sequences
--output-path emp-single-end-sequences.qza
I get the following message:

And if I paste the command without paying attention to the message, the error that comes up is the following:

I hope I have explained myself well and that you can help me. Thank you for your time!


Welcome to the :qiime2: Forum!

I think the message is normal in your context: you are directly copying and pasting from the tutorial, and the newlines trigger the message because your system detects you are pasting potentially separate commands that may be dangerous (and you have root privileges activated in your terminal so that can be really dangerous if you are not sure about what you are doing). Although you are okay copying and pasting commands from official QIIME 2 tutorials (they are safe commands written by nice people), as an advice it is better to type the commands yourself - not only for security reasons, you also learn more that way.

Regarding this:

I assume you are following the Moving Pictures tutorial since the command is the same. Are you using the tutorial data or your own data? If it is your own data, it is quite likely that you already have demultiplexed files, or paired-end (the tutorial uses multiplexed single-end data). In such cases, you need to edit the command to correctly import your sequences.

If you are using tutorial data, can you do ls ~/Escritorio/qiime2-paula/emp-single-end-sequences/ and share the output with us?

Best wishes,



Disclaimer: I'm only another forum user, just like you. Please don't take my answer as a ground truth. A Forum Moderator would probably provide you with a more accurate answer.


Hello Paula,

Welcome to the forums! :qiime2:

I agree with Sergio's advice!

I would also add that understanding each error is important.

For extra help and context, I often paste errors into an LLM like ChatGPT or Google Gemini to explain what the error means and what to try next.

While the Qiime2 errors are only in English, some LLMs speak more languages.