feature-table summarize - interactive sample detail being weird in Safari


I'm running into a weird problem where the interactive sample detail for a table summary is not 'calculating' correctly. When I type in a read depth, not all corresponding samples are highlighted/included and the # samples retained reported is inaccurate. I'm also not able to type in read depths greater than the max frequency, which may be new but I don't recall from previous versions. I also notice that the samples are not sorted by their frequency as they used to be, which may be related to the problem.

  • Version of QIIME 2 you are running, and how it is installed (e.g. Virtualbox, conda, etc.)
    conda (Mac M) qiime2-amplicon-2024.2
  • What is the exact command or commands you ran? Copy and paste please.
    qiime tools import
    --input-path /Users/shaffer-local/Mycelia/Academia/Projects/allergy-microbes/data/GSMc/global_soil_myco_biom.biom
    --type 'FeatureTable[Frequency]'
    --input-format BIOMV210Format
    --output-path /Users/shaffer-local/Mycelia/Academia/Projects/allergy-microbes/data/GSMc/global_soil_myco_biom.qza

qiime feature-table summarize
--i-table /Users/shaffer-local/Mycelia/Academia/Projects/allergy-microbes/data/GSMc/global_soil_myco_biom.qza
--o-visualization /Users/shaffer-local/Mycelia/Academia/Projects/allergy-microbes/data/GSMc/global_soil_myco_biom.qzv

  • What is the exact error message, if applicable? If you didn't run the command with the --verbose flag, please re-run and copy-and-paste the results.

No error - issue is with output visualization

Thanks in advance,


Hello @Lichen, there is a known bug with the qiime feature-table summarize viz that we are working on patching. We should have a patch release soon that ought to resolve the issues you're seeing. I believe the inability to enter a number greater than max frequency is new intended behavior, but the rest is not.

Thank you! Sorry if I missed that somewhere. I did not see a related post.


No you're good, I don't think we posted about it anywhere yet, but we will when the patch is released.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.