# empty barplot at the end
**URL:** https://forum.qiime2.org/t/empty-barplot-at-the-end/11732
**Category:** User Support
**Tags:** taxonomy, barplot
**Created:** [September 29, 2019, 12:10pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732 "2019-09-29T12:10:33Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@amoltej](https://forum.qiime2.org/u/amoltej)
#### Post date: [September 29, 2019, 12:10pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/1 "2019-09-29T12:10:33Z")
Hello everyone,
This is pretty weird. I have been running Qiime pipeline and everything is running as expected until the last step of getting bar plots with the taxonomy.
1. I did core matrix phylogenetics using the following command -
> qiime diversity core-metrics-phylogenetic
> --i-phylogeny rooted\_tree.qza
> --i-table pet-table.qza
> --p-sampling-depth 15000
> --m-metadata-file metadata.tsv
> --output-dir core\_metrics\_results
Then after creating and training datasets from both SILVA and Greengenes I tried to create box plot using following command -
> qiime taxa barplot
> --i-table core\_metrics\_results/rarefied\_table.qza \ (#I used filtered table here#)
> --i-taxonomy taxonomy.qza
> --m-metadata-file metadata.tsv
> --o-visualization taxa\_bar\_plots.qzv
But my taxa\_bar\_plots.qzv does not show any bar plots just a empty plot. I tried to save that files .CSV format through Qiime View server but it gave empty CSV file. The bar plot qzv file is not empty though. The size of this file is \>9mb
I had to filter my rarefied\_table using -
> qiime feature-table filter-features
> --i-table core\_metrics\_results/rarefied\_table.qza
> --m-metadata-file gg\_13\_99\_taxonomy\_assigned.qza
> --o-filtered-table id-filtered-table.qza
Can somebody please point out what might be happening?
Thanks
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### Author:  [@ben](https://forum.qiime2.org/u/ben)
#### Post date: [September 29, 2019, 12:23pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/2 "2019-09-29T12:23:08Z")
Try to use a shallower depth in the core metrics command.
How did you rarefy your table? What depth?
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### Author:  [@amoltej](https://forum.qiime2.org/u/amoltej)
#### Post date: [October 1, 2019, 1:47am UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/3 "2019-10-01T01:47:49Z")
Hi, thanks for reply.
I tried using depth at 5000.
It still showing same results
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### Author:  [@ben](https://forum.qiime2.org/u/ben)
#### Post date: [October 1, 2019, 2:02am UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/4 "2019-10-01T02:02:45Z")
I would try two things:
1. From the rarefied table, try to visualize the # of features using the qiime command to convert the table from a \*.qza to \*.qzv
2. From the table from DADA2/Deblur, I would do a taxa bar plot from that table to see if you get the same results
Can you link the file through drop box for us to take a look at? Ben
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### Author:  [@amoltej](https://forum.qiime2.org/u/amoltej)
#### Post date: [October 4, 2019, 1:12am UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/5 "2019-10-04T01:12:21Z")
Hi Ben,
Thanks for suggestions.
> 1. the table from DADA2/Deblur, I would do a taxa bar plot from that table to see if you get the same result
Table from `qiime dada2 denoise-paired` shows the same results
> the rarefied table, try to visualize the # of features using the qiime command to convert the table from a \*.qza to \*.qzv
This is how the .qzv [file](https://www.dropbox.com/s/59foyz4m5lmkogr/rarefide.qzv?dl=0) looks like for the data
Thanks
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [October 4, 2019, 10:27pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/6 "2019-10-04T22:27:44Z")
@amoltej,
Sounds like a hardware issue. Sounds like your barplot is not rendering, quite possibly because it is too large to display on whatever system or browser you are using. See here:
> [@Taxa Bar Pot can't be viewed](https://forum.qiime2.org/t/taxa-bar-pot-cant-be-viewed/3119/3):
>
> Hi @pumpkin, What browser are you using? It's possible that the barplot is simply too large of an SVG to be rendered frowning Does running qiime tools view taxa\_bar\_plots.qzv say anything different in your browser? q2view (the website you are on) doesn't host any of the data, nor does it really have a server to inspect it, instead it sends your browser the code to do all of that work on it's own. That means that its URLs aren't exactly real locations, but something that is made up on the …
Try a different browser, a different machine, so somehow collapsing your data to reduce sample counts before viewing.
Good luck!
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### Author:  [@amoltej](https://forum.qiime2.org/u/amoltej)
#### Post date: [October 8, 2019, 6:03am UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/7 "2019-10-08T06:03:37Z")
Hi Thanks for the suggestion.
I have been trying to run it on different machine, and platforms. But everywhere I am getting same output - Empty plot
Does anyone have any other suggestion?
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [October 8, 2019, 9:06pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/8 "2019-10-08T21:06:52Z")
what browsers have you tried? can you share the QZV?
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### Author:  [@amoltej](https://forum.qiime2.org/u/amoltej)
#### Post date: [October 9, 2019, 1:43am UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/9 "2019-10-09T01:43:38Z")
I have tried Microsoft Edge, Chrome and firefox. [Here](https://www.dropbox.com/s/amr374j7zy396cs/taxa_bar_plots_5000.qzv?dl=0) is the file
Thanks
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [October 9, 2019, 8:04pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/10 "2019-10-09T20:04:42Z")
Hi @amoltej,
I have taken a look — this is not a hardware issue but rather the barplot is empty because the visualization has no data. This would suggest that, e.g., all features or samples were filtered out of your table.
The provenance does not really reflect the workflow you described above. It looks like you imported a file called "metadata.tsv" as a TaxonomyTSV format file and used that to filter features from the table... it is possible that you filtered out all features, resulting in an empty table. Is "metadata.tsv" a list of feature IDs? Do those feature IDs actually match features in your rarefied table?
In any case, I recommend using `qiime feature-table summarize` to examine the feature table you use as input to confirm that the table is not empty. If it is not empty, please share the QZV here so that we can examine.
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### Author:  [@ben](https://forum.qiime2.org/u/ben)
#### Post date: [October 9, 2019, 9:17pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/13 "2019-10-09T21:17:36Z")
I agree, sorry I took a look and it looks like there's no data.
I looked at where the data came from in the provenance and it's a bit weird:
it looks like that the taxonomy bar plots are pulled from several tables? Ben
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [October 9, 2019, 11:10pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/14 "2019-10-09T23:10:01Z")
> [@ben](#):
>
> it looks like that the taxonomy bar plots are pulled from several tables?
Just one table (that has been through a few steps to get to where it is). The step @Nicholas_Bokulich pointed out is highlighted here (see the details on the right side):
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [October 9, 2019, 11:12pm UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/15 "2019-10-09T23:12:18Z")
Also, I just noticed another thing in this provenance graph - @amoltej, you appear to be using the _rarefied_ feature table for the barplots. Once you sort out the issue of filtering, you should not use the rarefied table, but rather the unrarefied one --- no point in throwing away perfectly good data for a plot like this!
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [November 10, 2019, 5:12am UTC](https://forum.qiime2.org/t/empty-barplot-at-the-end/11732/16 "2019-11-10T05:12:21Z")
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