Problem with Qiime2 visualization

[Federica Fiorini]

Hi,

I am having issues visualizing qiime2 emperor plots (for example in this project: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=8e2295b73efa4bfdaf0a724b65f81fe0), as the following error message appear:

Something went wrong!

Error: Network error, recieved 500 from server.

Am I doing something wrong? How can I fix it?

I tried to download the .qza file and visualizing it through the web interface (qiime2 view), but I don´t get any plot, there are only "details" and "provenance" tabs available, no "visualization" tab, as if the data for generating the plot are missing?

Thanks a lot,

Federica

[Emily Gentry]

Hi Frederica,

For the particular Qemistree job you gave the link for, try downloading the Qiime2 data then go to the "output_folder" and drag and drop the "qemistree-itol.qzv" file into the Qiime 2 view web interface.  You will then be prompted to view the tree using iTOL and from the iTOL website, you will be able to interact with your qemistree dendrogram plot. In general, .qza files are data files while .qzv files are visualization files.  Hope this helps!!

All the best,

Emily

[Federica Fiorini]

Thank you, this is what I did, I also wrote it before, it is not the tree that I have problems in visualizing, but the emperor plots. Can you help with that?

[Shaurya Chanana]

I too am having trouble with the same error. My job is: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=920c8f7fb81540cebdcb1689fca19200 .And downloading the data, and dragging + dropping qzv or qza files both give me no options for "Visualization" (image attached). This is my first time using Qemistree and Qiime so I may have missed something but not entirely sure...

Best,

Shaurya

[Anupriya Tripathi]

Hi Shaurya, you can only visualize qzv file. Qza file are essentially zipped data files. Are you able to use qiime2 viewer for qzv visualization?

Anupriya Tripathi
Ph.D. Candidate
Labs of Rob Knight and Pieter Dorrestein
University of California San Diego

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[Shaurya Chanana]

Hi Anupriya,

Thanks for that information, good to know! My previous workflow did not have any qzv files!

I actually did a few small experiments to figure out the correct metadata formatting. Fair warning, I'm using Metaboscape 5.0. What I did last time was to use the FBMN workflow for Metaboscape. That allowed me view my custom defined ATTRIBUTES in cytoscape correctly. However, when I click on the [ View qiime2 Emperor Plots ] from my results of FBMN, then it finally does show up but now I get the occasional NaN for a category or weird categories (github issue linked here). In the metadata for qiime2, i see a number of weird looking categories that may originate from the "msms-only" file that metaboscape outputs.

Best,

Shaurya

[Federica Fiorini]

Hi  Anupriya and  Shaurya,

I am having the same issue, I have downloaded the qiime2 Emperor qzv files, but in the folder "qiime2_output" I have only .qza (and .tsv) files. I don´t understand how I should change my metadata table (if that´s the problem) in order for it to work.

Thanks for any help!

Federica

[Anupriya Tripathi]

Hi Federica, I downloaded the results from your job you shared above; it does look like you have qemistree-itol.qzv and I am able to visualize the tree. 

Were you asking about another job? 

In general, the metadata generated by the FBMN workflow works perfectly with Qemistree jobs. Hope this helps!

Anupriya Tripathi
Ph.D. Candidate
Labs of Rob Knight and Pieter Dorrestein
University of California San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/molecular_networking_bug_reports/e0c30b39-d376-48e8-b0c0-207d941f66dcn%40googlegroups.com.

[Federica Fiorini]

Hi Anupryia,

thanks for your answer. Actually I can see the Qemistree, but not the qiime2 emperor plots (I think there was some missunderstanding as I have opened this thread for this issue but then Shaurya had a similar error when visualizing the Qemistree).

Can you help me with that?

Thank you!

Federica

[Emily Gentry]

Hi Frederica,

Can you view the qiime2 emperor plots in the corresponding FBMN job or do you get the same error?

All the best,

Emily

[Federica Fiorini]

Hi Emily,

Unfortunately not, I cannot open it from the FBMN job (I get the error "Something went wrong! Error: Network error, recieved 500 from server."). So I tried downloading the folder to visualize it through the web interface (qiime2 view), but I don´t get any plot, there are only "details" and "provenance" tabs available, no "visualization" tab, maybe because I don't have the .qzv file? But how to generate it?

Thanks!

Federica

To view this discussion on the web visit https://groups.google.com/d/msgid/molecular_networking_bug_reports/cf0a6df7-dfc9-4782-ad55-c1839c4a439bn%40googlegroups.com.

[Emily Gentry]

Federica,

Could you please send the link to your FBMN job? This will help troubleshoot.  There could be an issue in your metadata.

All the best,

Emily

[Federica Fiorini]

Yes sure, for example in this project: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=8e2295b73efa4bfdaf0a724b65f81fe0)  
thanks,

Federica

[Oliver Gericke]

Hi, It seems the qzv-files are missing in the usual output (qiime2_emperor.qzv and qiime2_biplot_emperor.qzv) - you will be able to visualize your data at Qiime view when this is fixed.

To view this discussion on the web visit https://groups.google.com/d/msgid/molecular_networking_bug_reports/7596d372-9ea3-4c50-9b98-f45be50add93n%40googlegroups.com.

[Federica Fiorini]

Ok thanks a lot!