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

User Support
1

Hello,

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,

Justin

2

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.

3

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

2 Likes
4

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

5

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