Problem viewing page created with "qiime tools extract "

Technical Support
1

Hi,

I created a barplot artefact using the following commands:

qiime taxa barplot \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --m-metadata-file metadata.tsv \
  --o-visualization taxa-bar-plots.qzv

It worked as expected. I need to extract the results to present them in a similar way that the qiime viewer presents them so I ran:

qiime tools extract --input-path taxa-bar-plots.qzv --output-path taxonomy_barplot

I created the expected directory with the extracted data. But when I open the web page in taxonomy_barplot/.../data/index.html, it only presents the qiime logo.

I had a look at the javascript console to check for errors in my browser. I get a series of errors like this:

The resource from “.../taxonomy_barplot/.../data/level-6.jsonp?callback=load_data” was blocked due to MIME type (“application/octet-stream”) mismatch (X-Content-Type-Options: nosniff).

I also checked that the data are there in the network inspection tool of my browser. It returns 200 on the level-*.jsonp files and They are not empty.

I also took the taxa-bar-plots.qzv file and loaded it successfully in the qiime viewer.

What am I doing wrong?

Cheers,

7

Hello @pdupont

What version of QIIME 2 did you run these commands on? Additionally, what browser are you using? I would recommend you try any other browsers you have available and see if any of them work.

Thank you

9

Hi,

I use qiime 2020.8. I installed it using conda.
I tried both Firefox and Chrome with the same result. I'm on linux so these are the only ones I have...

Is anybody able to reproduce my issue?

Cheers,

10

@pdupont - does the following command work:

qiime tools view taxa-bar-plots.qzv

?

11

Qiime is installed on a corporate network on a computation Linux cluster without X server so I can't test that, sorry. This is the main reason why I am extracting the data...

12

:+1:, makes sense. Well, there isn't too much we can do to help you configure your browser, I'm not even sure if its possible. Personally, I would just use view.qiime2.org to view the results - no network connection is required, your data never leaves your computer (its a server-less static page that leverages your browser to unzip and view your results). Just transfer the results to a machine with a graphical user environment, go to view.qiime2.org, and load the visualization there.

13

Hi,

It's what I have been doing so far. I am not sure that it is a problem of browser config though. The error message seems to indicate that it could be a MIME type issue...

14

Really? What you described above is a little different, specifically, the process of extracting the QZV, and opening index.html. Can you confirm what exactly it is you're doing? If you are exporting and opening index.html, please try the steps I suggested above, by viewing at view.qiime2.org. Thanks!

15

I do the extraction and because I can't see the data on somes pages, including the one from the extraction of taxa-bar-plots.qzv, I used the view.qiime2.org on the qzv file and it works so it is the solution that I have used so far.

16

Perfect, sounds like you're all set then!

:qiime2:

17

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