Please kindly assist, I am trying to use Qiime2 to convert a tsv table to a qzv/qza and I keep getting errors. I added a column to my metadata file in google sheets and i converted the table to a tsv file. now i want to convert the table to a qza/qzv file.
Thanks for reaching out! Can you please provide us with more information? More specifically:
- Is this a metadata file? If so, what are you trying to do with your metadata? Are you trying to run
metadata tabulate? Or use it as a parameter in another command? Outside of
metadata tabulate you cannot turn your metadata file into a QIIME 2 Artifact.
- What error message(s) are you receiving?
This information will help us to better assist you. Thanks!
yes, that's what i was trying to do. I have a metadata file in the qza format and i wanted to add an extra column to the table. i downloaded the table and made copied the information to a google sheet. i edited the google sheet and now i want to convert the google sheet to a qiiime qzv table
You should be able to download your excel file as a .tsv and use that in qiime2.
Then you should be able to generate a .qzv by running this command:
qiime metadata tabulate
Here is an example of this from our tutorial: Metadata in QIIME 2 — QIIME 2 2022.2.0 documentation
Hi @cherman2 let me try that, thank you
[quote="cherman2, post:4, topic:26602"]
qiime metadata tabulate
i am getting an error message which says, 'qiime is not recognized as an internal or external command', operable program or batch file
Make sure that you have your qiime env activated!
it seems like it is, but once i start to put in commands, then it gives that error message.
That is weird! I would try uninstalling and reinstalling your qiime2 env. Looks like something got messed up in the qiime installation!
You can't run qiime using windows. You can either install windows subsystem for linux, or use another computer that runs linux or macOS.
hello, thank you. i installed windows subsytem for linux and I have been installing qiime2 following the respective prompts for windows subsytem for linux. at some point if i ran qiime help/ info, I could see that qiime was installed but not anymore
We need more information to be able to help! Could you please give us a step by step of what you are doing to activate your qiime2 env?
Could you also provide what error is occurring that is letting you know that qiime2 isn't installed?
So firstly, i opened the command prompt (Miniconda 3), then i typed 'conda activate qiime2-2023.2'
when i do that, it then says 'qiime is not recognized as an internal or external command', operable program or batch file'
it also does the same when i type 'qiime --help'
You are writing
qiime2-2023.5 but the name of your environment is
This doesn't matter however, because as stated previously, you can not run qiime on windows. You said you installed windows subsystem for linux. Now you need to open a shell to that operating system and enter your commands there.
oh i see, thank you. let start everything all over again and see that goes
hello @colinvwood @cherman2 , i have been able to install qiime2 and i was able to create some folders and download the data for the importing data tutorial. I downloaded them to my root directly. However, I was wondering if you can help on how I can change directories or say view what's on my Desktop or what's in a certain folder on a Windows (WSL) . for example I ran this: (qiime2-2023.5) root@Priscillar:~# cd ~/Desktop
-bash: cd: /root/Desktop: No such file or directory
and I got the "no such file directory", I keep getting that error no matter how i change the command.
It looks like there may be some confusion about interacting with a linux command line. This book would be a good place to start.
Another piece of information that is going to help is that your windows file system is probably mounted at
/mnt/c inside WSL.
Here's something I do which I think you may find helpful:
When running WSL, you can run this command to open up the current Linux working directory in the Windows Explorer
Explanation: In Linux, the dot
. means the current working directory.
So this command just tells the Windows File Explorer to open up your current folder.
I hope this helps! There's a lot to learn about Linux, but a little bit goes a long way.
We are happy to help you get started so you can use Qiime2.
Thank you, i will give that a try