Error running alpha diversity (qiime2 2024.2)

[adoty3 (Alex Doty)]

Hi, I am trying to run alpha diversity on metabolomics data using the following input:

qiime diversity alpha \
--i-table FEATURE-BASED-MOLECULAR-NETWORKING-9cac7690-download_emperor_data-main.qzv \
--p-metric shannon \
--o-alpha-diversity shannon_vector.qza

After attempting to run I receive the following errors:

(1/4) Missing option '--i-table'.

(2/4) Missing option '--p-metric'.

(3/4) Missing option '--o-alpha-diversity'. ("--output-dir" may also be used)

(4/4) Got unexpected extra arguments ( --i-table FEATURE-BASED-MOLECULAR-

NETWORKING-9cac7690-download_emperor_data-main.qzv --p-metric shannon

--o-alpha-diversity shannon_vector.qza)

Any guidance would be greatly appreciated! Apologies if this question has already been answered. I did not see anything about this topic on this version of qiime when searching the forums.

Thanks!

[Oddant1 (Anthony Simard)]

Hello @adoty3, this seems to be some sort of shell error, the following formatting (how you had it):

qiime diversity alpha \
--i-table FEATURE-BASED-MOLECULAR-NETWORKING-9cac7690-download_emperor_data-main.qzv \
--p-metric shannon \
--o-alpha-diversity shannon_vector.qza

ought to work assuming your input table is the correct type. Can you please copy the command as I wrote it there, paste it into your terminal, and rerun it?

If that doesn't work can you please try renaming your artifact probably to something with no - or _ characters in the name?

[adoty3 (Alex Doty)]

Hi Anthony,

Thank you for your help! I was able to run the analysis after changing my file name to one with no - or _. I also realized that I was using the incorrect file format when troubleshooting.

Thanks again for your help!