metadata tabulate script will not run

Hey !

Guys, I need your help. I am almost getting a crazy to fix this script. I am trying to run a script for visualization of metadata. But, it’s not running. I was wondering, where I could have made a mistake? Plz, help me !

here is the script.

#$ -S /bin/bash
#PBS -l walltime=100:00:00
#PBS -d.

source /home/shonb/miniconda3/bin/activate qiime2-2020.8
qiime metadata tabulate
–m-input-file denoising_stats.qza
–o-visualization tabulated-denoising_stats.qza
source /home/shonb/miniconda3/bin/deactivate

Could you try to provide tabulated-denoisingstats.qzv as an output instead of tabulated-denoising_stats.qza?

@timanix is right. You should change your file extension from .qza to .qzv only in output parameter. The letter is for visualization (end letter of the three letters [V] in .qzv stands for visualization but you have applied .qza. It is what exactly you need.

Use this:

qiime metadata tabulate
–m-input-file denoising_stats.qza
–o-visualization tabulated-denoising_stats.qzv

Happy with your Qiiming.

Thanks. But it’s not working.

Share the error and your command here.

Actually I am not getting an error and output file. But usually after submitting the script in cluster, I should get an error and output file. But here, in this case, I’m not getting anyone from both. Why?

I am not sure what did you say that I got correctly. It is difficult to predict what issue you have faced. In my opinion, you should share more info like command, screenshot, etc. Just wait for the professional admins to consider this case.
Good luck

One thing crossed my mind. I think you have not put "" or backslash character in end of parameter(s). In other words, you disregarded paths. Please test this command below:

qiime metadata tabulate
--m-input-file denoising_stats.qza
--o-visualization tabulated-denoising_stats.qzv

Screenshot from 2021-01-24 20-48-56

Reply me what did you get.

Nothing happened and respectively it didn't work.

Excuse me, is it Qiime2 environment?

Hi @ShonB - one of the official @moderators will be with you soon. In the meantime, can you please provide us an example of the error you are observing? It is not clear to me from the thread.

@TurboQiimer - thank you for your assistance, we appreciate it. The moderator team is happy to take this over, though.


1 Like

Hey. Thank you for cooperation. I have fixed it.

Almost have forgotten to point -cwd. Without pointing -cwd, it wasn’t running.

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