qiime feature-table filter-features-conditionally

Technical Support
1

Hi,
I amtrying to filter those taxa that are present in less that 25% of my samples at a frequency less than 0.01%.
I used the command qiime feature-table filter-features-conditionally, but it did not wors *see below the error message.
How can I proceed?
Thank you very much

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Is this post about a Technical Support Question? Those include error messages observed while running QIIME 2, errors observed while installing QIIME 2, or any other "software" related problem or bug. Please do not post questions here that have to do with interpretation of results, or general discussion.
Yes

Before posting, please make sure you have the following information available, in order for us to help you in a timely manner:

  • Have you searched for the problem on the forum? It is rare that we see a new question asked, so make sure you do your homework before asking for us to commit our time to helping you.
    Yes

  • Have you reviewed the QIIME 2 Forum Glossary?
    Yes

  • Version of QIIME 2 you are running, and how it is installed (e.g. Virtualbox, conda, etc.)
    qiime2-2020.8

  • What is the exact command or commands you ran?
    qiime feature-table filter-features-conditionally
    --i-table table.qza
    --p-abundance 0.0001
    --p-prevalence 0.75
    --o-filtered-table table-prevalent.qza \

  • What is the exact error message?
    Error: QIIME 2 plugin 'feature-table' has no action 'filter-features-conditionally'.

1 Like
2

Hi @favaf,

Welcome to the :qiime2: forum! Thank you for going through the checklist so carefully!

I know filter-features-conditionally was added recently, so its possible its not in that qiime2 release. (I dont remember which version exactly.) You can check all the commands in the feature-table plugin by running

qiime feature-table

If the function isn't included in the plugin, you may need a later version.

Best,
Justine

1 Like
3

Dear Justine,
yes, that might be the problem. When I run the help function on the feature-table command I did not find the option filter-features-conditionally.
I might try and see if it works when installing a more recent version.
My current version is qiime2-2020.8.
Thank you very much for your suggestion!
Francesca

1 Like
4

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