# Visualize with Krona error? Use Krona Pie Chart instead! **URL:** \ **Category:** Resources\ **Tags:** text-manipulation, metagenomics, tool-help, open-tutorial-issue, krona-text\ **Created:** [December 9, 2024, 3:15am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111 "2024-12-09T03:15:36Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![Barry](https://avatars.discourse-cdn.com/v4/letter/b/958977/32.png) [@Barry](https://help.galaxyproject.org/u/Barry)\ **Post date:** [December 9, 2024, 3:15am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/1 "2024-12-09T03:15:36Z")
I am trying to plot a Krona chart from a Kraken2 report, but I keep getting the following error: /cvmfs/main.galaxyproject.org/shed\_tools/toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona\_text/b14f1444e464/krona\_text/runKrona.sh: line 27: ktImportText: command not found ---
**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 9, 2024, 11:30pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/2 "2024-12-09T23:30:11Z")
Welcome, @Barry Which server you are working at? Would you like to share the history if at a public Galaxy server so we can help to troubleshooting this? Please see the banner at this forum, or here directly to learn what information we are looking for. → [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469) Thanks! 🙂 ---
**Author:** ![Barry](https://avatars.discourse-cdn.com/v4/letter/b/958977/32.png) [@Barry](https://help.galaxyproject.org/u/Barry)\ **Post date:** [December 10, 2024, 1:08am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/3 "2024-12-10T01:08:40Z")
I was on the global server when the error occured. However, the error did not appear when I ran the same krona visualisation program on the Galaxy AUS server ---
**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 10, 2024, 6:18pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/4 "2024-12-10T18:18:19Z")
> [@Barry](#): > > I was on the global server when the error occured. Hi @Barry – If you could share the URL for the server, we can check to see if there is a technical problem, and fix it. Find this at the very top of your web browser. [UseGalaxy.org](http://UseGalaxy.org) or [UseGalaxy.eu](http://UseGalaxy.eu)? > [@Barry](#): > > However, the error did not appear when I ran the same krona visualisation program on the Galaxy AUS server This server is the [UseGalaxy.org.au](http://UseGalaxy.org.au) server, correct? This server has slightly different resources for AU researchers but we can compare once we know where the error is happening. Your history share link would include the URL, too, which is why I asked for it. Thanks! 🙂 ---
**Author:** ![Barry](https://avatars.discourse-cdn.com/v4/letter/b/958977/32.png) [@Barry](https://help.galaxyproject.org/u/Barry)\ **Post date:** [December 11, 2024, 12:52am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/5 "2024-12-11T00:52:22Z")
Hi! The URL for the server with the error is as follows: > **[Galaxy](https://usegalaxy.org/datasets/f9cad7b01a47213507fa25a5bf3ad97c/preview)** > > Galaxy is a community-driven web-based analysis platform for life science research. The server that runs Krona without error is indeed [UseGalaxy.org.au](http://UseGalaxy.org.au). ---
**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 12, 2024, 6:56pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/6 "2024-12-12T18:56:38Z")
Hi @Barry Thanks for sharing the history! I see the problem. Krona can only work with tabular data that has a whole number “count” in the first column, then labels in the other columns. So if you ever get an error – this is what to look at – is my data formatted in a way that the tool can covert automatically (mothur taxonomy can be converted this way) or do I need to do some data manipulation on my own first? **What to do** Reformat your Kraken report to a tabular file that the Krona tool can use. This is what is in your history as the error. I’m guessing that a different implementation of Krona was used at AU (search the tool panel with “krona” to see all choices at any particular server). - **Krakentools: Convert kraken report file** to krona text file → [link at ORG](https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2) - **Visualize with Krona** Visualise any hierarchical data → [link at ORG](https://toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1) And, to complicate it, there are _even more ways_ to do this too, including custom ways! If interested, please scroll down on the tool forms to find more instructions: examples of how the inputs files are formatted and links to tutorials with examples. For general text manipulation, we also have some tutorials that might be interesting to you or anyone else reading this later. See → [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=olympics) (query=olympics), with prior Q&A here at #text-manipulation Hope this helps! 🧑‍🔬 ---
**Author:** ![Barry](https://avatars.discourse-cdn.com/v4/letter/b/958977/32.png) [@Barry](https://help.galaxyproject.org/u/Barry)\ **Post date:** [December 13, 2024, 5:48am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/7 "2024-12-13T05:48:47Z")
Hi, I had done exactly what you mentioned for job number 60 on the history, yet the error persisted. The converted krona text file does indeed have the whole number “count” as the 1st row (job number 59). ---
**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 13, 2024, 6:23pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/8 "2024-12-13T18:23:23Z")
Hi @Barry The history share link isn’t working for me. Could you please generate it again? Maybe toggle it on/off? Thanks! ---
**Author:** ![Barry](https://avatars.discourse-cdn.com/v4/letter/b/958977/32.png) [@Barry](https://help.galaxyproject.org/u/Barry)\ **Post date:** [December 17, 2024, 12:54am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/9 "2024-12-17T00:54:44Z")
Here is the link to the history. Thank you for your help so far! > **[Galaxy](https://usegalaxy.org/published/history?id=bbd44e69cb8906b54ed23d9f3b129333)** > > Galaxy is a community-driven web-based analysis platform for life science research. ---
**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 17, 2024, 8:09pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/10 "2024-12-17T20:09:52Z")
Hi @Barry It does seem like that version of Krona has a dependency problem! I’m reviewing and if true, we’ll get that fixed up at the ORG server. However – you do not need to wait because there is another version of Krona that works on your data. See the last result dataset 122 in the copy of your history that I am sharing back. It uses the same input dataset 69 and your failed run in dataset 70. So the only extra step was changing the tool to use. - _admin edit: unshared history purged from server._ - Using **Krona pie chart** from taxonomic profile ([link at ORG](https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0)) - Update: bug tracking ticket → [Fix ktImportText dependency for krona\_text · Issue #900 · galaxyproject/usegalaxy-tools · GitHub](https://github.com/galaxyproject/usegalaxy-tools/issues/900) I’ll leave this shared until you get a chance to see or import it. I’ll also come back and post a bug fix ticket later today – done! see above. Thanks for all the follow up! Very helpful. 🚀 ---
**Author:** ![Barry](https://avatars.discourse-cdn.com/v4/letter/b/958977/32.png) [@Barry](https://help.galaxyproject.org/u/Barry)\ **Post date:** [December 18, 2024, 1:18am UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/11 "2024-12-18T01:18:20Z")
Hi! It works! Thanks so much! ---
**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 20, 2024, 7:18pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/12 "2024-12-20T19:18:27Z")
Great @Barry thanks for letting us know! That other version of Krona is older and needs some special handling on the server – we’ll work on that. 🛠 ---
**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:** [August 6, 2025, 10:52pm UTC](https://help.galaxyproject.org/t/visualize-with-krona-error-use-krona-pie-chart-instead/14111/13 "2025-08-06T22:52:42Z")
Update: always use the other tool now. See → [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)