# Krona troubleshooting

**URL:** <https://help.galaxyproject.org/t/krona-troubleshooting/16362>\
**Category:** Uncategorized\
**Tags:** troubleshooting, taxonomy\_krona\_chart\
**Created:** [October 6, 2025, 7:00pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362 "2025-10-06T19:00:36Z")\
**Posts on this page:** 16\
**Page:** 1

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**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 6, 2025, 7:00pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/1 "2025-10-06T19:00:36Z")

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HI, not sure how to start a new query so will add this one.

I am trying to create a Krona chart but all I can see in snapshot is an empty circle.

The input file looks fine. Several columns with heirarchical taxonomy.

Any ideas ?

This is the html file

[https://help.galaxyproject.org/t/basic-edna-worklow/14340/6?u=adam\_hillier](https://help.galaxyproject.org/t/basic-edna-worklow/14340/6)

Thanks

Adam

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 6, 2025, 7:02pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/2 "2025-10-06T19:02:52Z")

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This is the Krona html file if it helps

> [@Basic eDNA worklow](https://help.galaxyproject.org/t/basic-edna-worklow/14340):
>
> Hi, would like to use Galaxy to build an eDNA workflow pipeline to process Metabarcoding data from Illumina. Is this possible or are there other open source tools available to do this ? Basic steps needed : Read demultiplexed FASTQ files Merge paired reads Filter and trim Cluster Map to BINs in BOLD or another database Outputs taxa lists for each sample.

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 7, 2025, 4:35pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/3 "2025-10-07T16:35:18Z")

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Hi @Adam_Hillier

Glad to learn you have made some progress! I moved this over into a new topic so we can focus on the new tool error.

If you want to share your history with the work, we can try to help resolve the error. How to generate a history share link is explained here → [FAQ: Sharing your History](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) or you can capture screenshots and post those instead as explained in here → [How to get faster help with your question](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469). If you post screenshots – please try to capture all the details – the server URL, the full tool name/version, a peek at the input file, the parameters used, and the full log messages expanded. That’s a lot of information and why we suggest to share the history since it includes everything all together. 🙂

If you want to troubleshoot it yourself first, we have some prior Q&A about one common issue: choosing the wrong Krona tool! See here for the details → [Error with Visualize with Krona tool? Use Krona Pie Chart instead!](https://help.galaxyproject.org/t/error-with-visualize-with-krona-tool-use-krona-pie-chart-instead/14562) with more at [Search results for 'krona' - Galaxy Community Help](https://help.galaxyproject.org/search?q=krona)

Let’s start there and please let us know if you resolve this! 🧑‍🔬

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 5:19pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/4 "2025-10-07T17:19:30Z")

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HI Jenna,

Thanks for picking this up.

I have looked in to inside and outside Galaxy and haven[t had much luck. I have also looked on online forums. It seems to be a known issue but I can’t fond the answer.

It looks like Krona plots should should be very easy. I will get back to you with the history and screen shots of the input file format and what I see from Galaxy.

In the meantine, can you tell me a bit about how Galaxy is set up ?

Is it all managed at Penn State Uni ?

Where does the funding come from (the development costs, the support and the computing) ?

Any idea how many users globally and in the UK ?

How many people in the support team like you ? You seem very responsive !

I have a lot of work coming up and will have to learn to use Galaxy as the bioinformatics platform I have used before (mBRAVE) won’t work for what I am doing next. I get the feeling Galaxy will be perfect.

Adam

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 5:25pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/5 "2025-10-07T17:25:27Z")

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Hi Jenna,

One more question. Are Nextflow your main ‘rivals’ so to speak ?

[https://mail.google.com/mail/u/0/#inbox/WhctKLbmpGrcvTVNCtLfndwKbTTRHfvszHqxTQthpCnLrwsvHTfCdslclkJRdfCVmxPbdcL](https://mail.google.com/mail/u/0/#inbox/WhctKLbmpGrcvTVNCtLfndwKbTTRHfvszHqxTQthpCnLrwsvHTfCdslclkJRdfCVmxPbdcL)

Adam

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 5:46pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/6 "2025-10-07T17:46:37Z")

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HI Jenna,

Attached is an example of the kind of work I do.

I just found the comparison matrix below which is quite helpful.

As I am self taught I want something easy to use (not programming language level if possible) and Galaxy seems to tick that box perhaps more than any other.

My workflows will be pretty straight forward I think (compared to what I imagine others do anyway).

Are you aware of anyone else in the Galaxy community like me ? Ie an amatuer doing biodiversity DNA metabarcoding studies of various kinds.

Adam

 ![9A4AC81C-D173-4E95-B4E7-9104C52675CA.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/5/5d5c60a335e931a43375e3a220e81ef8e049cdc0.jpeg)

(Attachment River Ivel eDNA study FBA Science Article Draft for Final Review - October 1st .docx (2).pdf is missing)

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 7, 2025, 5:47pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/7 "2025-10-07T17:47:07Z")

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We can help to troubleshoot here. Issues are usually with how the data is formatted versus what was expected. That same job (inputs, parameters, tool) would fail anywhere, not just in Galaxy, since the hosted tool is still just the original underlying tool run on a computing cluster somewhere. 🙂

For your other questions, please start here for the bigger picture → [https://galaxyproject.org](https://galaxyproject.org)

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 5:58pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/8 "2025-10-07T17:58:05Z")

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HI Jenna,

This is my work flow. which is very simple,

 ![D3168359-0CCC-4B33-BB0B-99FD396D9FBD.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/1a043c0077c0f9cb79ee17acf901d13cb31a629a.jpeg)

This is my input data table which looks fine

 ![E8BB11D6-6933-4CA8-A739-74891E13C97F.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/ab46c526b37229b296757766a8e51e75081132b2.jpeg)

This is what I get from Krona Plot

 ![63DB1C17-6D89-4B04-8A43-384A293DB692.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/aef331a6c8c9cc54c881835f57b2cbbdbd3bb68e.jpeg)

This is what i see when I press screenshot. The Krona plot is empty. No suspicious messages.

 ![EF966D3E-1A2C-40D1-96D8-FF3368147923.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/68c8a6ed5ab1ac9590fc2903edb0cf40fd6ffb6c.jpeg)

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 6:01pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/9 "2025-10-07T18:01:30Z")

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Yes, I agree the problem here is probably ‘underneath’ Galaxy.

I get the same problem when I run Krona plot from a bash terminal.

Adam

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 7, 2025, 6:07pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/10 "2025-10-07T18:07:20Z")

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Thanks for sharing the screenshots @Adam_Hillier ! Very helpful and I see the problem. Krona is looking for a count value in the first column, then categories in the others. Your file is missing that first value.

This is the **Help** from the tool form (scroll down to find this, plus links to the original tool author documentation, any GTN tutorials that tool is included in, plus sometimes topic at this forum).

> Krona text input requires a tab-delimited file with first column being a count, and the rest representing the hierarchy

 ![Screenshot 2025-10-07 at 11.02.30 AM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/e7835c1c396e27c3fa627a85d164ad611db2dd97.png)

* * *

Then, for a full Metagenomics pipeline, we had a topic recently where I broke down where to access resources like use guides, tutorials, and workflows with that context. I think this will address the other parts of your larger questions. → [Kraken2 reference database for shotgun sequencing data - #4 by jennaj](https://help.galaxyproject.org/t/kraken2-reference-database-for-shotgun-sequencing-data/16319/4)

Hope this helps! 🙂

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 6:22pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/11 "2025-10-07T18:22:53Z")

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HI Jenna,

To be honest I did not find [https://galaxyproject.org](https://galaxyproject.org/) very useful at all to answer my questions. Thee should be a font page explaining what Galaxy is about.

Is it about bioinformatics ?

It says it can be used for analysing data. Bioinformatics data only ? Anything else ? What about astronomical data ?

I didn’t really get beyond that.

I explored a few other areas the they took me down rabbit holes.

So I still don’t know what it does, what it doesn’t do, why it exists, who is behind it and who it’s for.

Is it really for PhDs/postdocs sat Penn State Uni studying molecular biology for medical research ?

It’s a bit worrying if I cant find any information on the above on the front page or the About section.

Adam

 ![A2FDEE5F-CD18-416B-9D8C-D85FB010303E.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/c82d399c6559943a85a23ecab70576b93938ea2e.jpeg)

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 6:31pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/12 "2025-10-07T18:31:13Z")

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I see.

For eDNA you can only detect presence. No abundance.

If I added a column of 1s would the plot make any sense.

Adam

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<div class="post-metadata">

**Author:** ![Adam\_Hillier](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/adam_hillier/32/6564_2.png) [@Adam\_Hillier](https://help.galaxyproject.org/u/Adam_Hillier)\
**Post date:** [October 7, 2025, 6:52pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/13 "2025-10-07T18:52:47Z")

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All sorted.

Many thanks !

Adam

 ![3D354671-62E5-4827-9FD1-CA569B8801D4.jpeg](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/778b477620fcfe9553575a973e9497d786bd976d.jpeg)

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 7, 2025, 7:39pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/14 "2025-10-07T19:39:00Z")

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Hi @Adam_Hillier

On the homepage, under **Citing Galaxy** , you can read our latest publication for more details:

- [https://galaxyproject.org/citing-galaxy/](https://galaxyproject.org/citing-galaxy/) \<\< see for more publications

- [https://academic.oup.com/nar/article/52/W1/W83/7676834](https://academic.oup.com/nar/article/52/W1/W83/7676834) \<\< 2024 Update

- To get a better idea of scientific/regional scope (“Using Galaxy”) maybe visit the Special Interest Communities page → [Special Interest Groups (SIG) - Galaxy Community Hub](https://galaxyproject.org/community/sig)

- Then for the architecture (“Creating Galaxy”), the Working Groups are a good summary → [Galaxy Working Groups - Galaxy Community Hub](https://galaxyproject.org/community/wg/)

- With public assets listed here [Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub](https://galaxyproject.org/use/), but these are just a fraction of what is used and exists.

* * *

* * *

Back to the Krona plot, I guess you could add in a “1” to each column. That would allow you to browse the categories present in your file in the circle graphic, if that is your goal and a table view is not enough?

Or, you might want to back up and try for a more interesting visualization! How to exactly do this would depend on where the taxonomy information came from. But one example pathway is: **Tools: Braken or Kraken2** → **Tools: ToolDistillator** (to reformat to JSON) → **Visualizations: Unipept Taxonomy Viewer**.

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [December 3, 2025, 6:56pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/15 "2025-12-03T18:56:30Z")

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A post was split to a new topic: [Taxonomy workflows: reads to taxa](https://help.galaxyproject.org/t/taxonomy-workflows-reads-to-taxa/16541)

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [December 3, 2025, 6:56pm UTC](https://help.galaxyproject.org/t/krona-troubleshooting/16362/16 "2025-12-03T18:56:35Z")

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