qiime metadata tabulate denoising stats file does not contain any stats

Hi,

I can get the following command to run successfully, but the output is confusing.

qiime metadata tabulate
--m-input-file denoising-stats.qza
--o-visualization denoising-stats.qzv

When I look at the .qzv file on qiime visualize my data only includes sections 'sampleid' and 'sampletype'. There are no sections for input, filtered, merged reads, etc. like I see in the tutorials. Here are screenshots of my output vs the expected from the Fecal microbiota transplant (FMT) study tutorial. I have been following this tutorial and prior to this step I trimmed sequences with dada2.

Any ideas on what could be causing this? I'm wondering if maybe I overtrimmed my samples?

Thanks!

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Hi @mkc206,

This is certainly unusual - do you mind sharing your denoising-stats.qza file with me? And your demux summarize visualization as well, if you don't mind? Feel free to send them to me in a DM if you'd prefer not to share them publicly. This will give me a better understanding of your data and whether you may have overtrimmed - thanks! :lizard:

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Okay I may have figured out the issue - I reran everything and realized when I got the the 'qiime metadata tabulate' step I've been getting this error and 'solving' it by providing a .tsv file.

There was an issue with loading the file /temp/West22_denoising_stats.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): /temp/West22-stats-dada2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: Metadata in QIIME 2 — QIIME 2 2022.11.1 documentation

Apologies for not listing the proper file before. It had been a bit since I had run this command and I ended up posting the code from a tutorial (since it seemed like it was quite simple with their file name structure - my mistake!).

So, it seems like the problem is that I provided the wrong file and that's what's causing a difference in the visualization output, and the real issue here is that I need to fix my .qza file. I'm just confused because I thought that Keemei was for .tsv files.

After looking at all of my demux summarize files across my meta-analysis I chose to trim at 35 (f) and 13 (r), and truncate at 180 (f) and 113 (r).

I'm attaching those files for you here. Thanks for taking a look at this!
West22_demux.qzv (317.7 KB)
West22_denoising_stas.qza (14.3 KB)

Turns out the reason it didn't work with my .qza file is because there was character difference between the file name and what I had in the script. Sorry to have wasted your time. The lesson here is to always post the code and file names you actually use :sweat_smile:

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