# How to view Kraken2 Results in Krona? **URL:** \ **Category:** usegalaxy.org support\ **Tags:** troubleshooting\ **Created:** [April 23, 2019, 12:13pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137 "2019-04-23T12:13:15Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![vmevada102](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vmevada102/32/433_2.png) [@vmevada102](https://help.galaxyproject.org/u/vmevada102)\ **Post date:** [April 23, 2019, 12:13pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/1 "2019-04-23T12:13:15Z")
Hello all, I am working in the community analysis of the metagenomics data. Kraken2 is complied and merge all its previous separate tools to run in Galaxy. The problem i am facing is that, it will not generate file to view results in the Krona Pie chart. It is most essential step to visualize the results. kindly suggest some solution or update for the above said problem. ---
**Author:** ![dave](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dave/32/32_2.png) [@dave](https://help.galaxyproject.org/u/dave)\ **Post date:** [April 23, 2019, 1:08pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/2 "2019-04-23T13:08:34Z")
Good morning, You can convert Kraken data to a format compatible with Krona by using the `Convert Kraken data to Galaxy taxonomy representation` tool, available at [usegalaxy.org](http://usegalaxy.org) and .eu, as well as installable from the [toolshed](https://toolshed.g2.bx.psu.edu/view/devteam/kraken2tax). I haven’t checked whether it’s compatible with kraken2 output, but since I was involved in its development, it would fall on me to update it if it isn’t. ---
**Author:** ![vmevada102](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vmevada102/32/433_2.png) [@vmevada102](https://help.galaxyproject.org/u/vmevada102)\ **Post date:** [April 23, 2019, 1:42pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/3 "2019-04-23T13:42:22Z")
That tool supports the kraken results… It is not working for the results of Kraken2. ---
**Author:** ![dave](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dave/32/32_2.png) [@dave](https://help.galaxyproject.org/u/dave)\ **Post date:** [April 23, 2019, 2:21pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/4 "2019-04-23T14:21:20Z")
Good to know. We’ll have to create one for Kraken2, then. ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 6:10pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/5 "2019-04-24T18:10:23Z")
Hi , I am trying to install kraken2 databases through data manger. Its giving me an URL error to download the databases. Can you please check if the URL provided is correct?. here is the error: Fatal error: Exit code 1 () Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/bin/kraken2 line 16. Traceback (most recent call last): File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_minikraken.py”, line 100, in main() File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_minikraken.py”, line 93, in main target\_directory, File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_minikraken.py”, line 44, in kraken2\_build\_minikraken % minikraken2\_version File “/usr/lib64/python2.7/urllib2.py”, line 154, in urlopen return opener.open(url, data, timeout) File “/usr/lib64/python2.7/urllib2.py”, line 437, in open response = meth(req, response) File “/usr/lib64/python2.7/urllib2.py”, line 550, in http\_response ‘http’, request, response, code, msg, hdrs) File “/usr/lib64/python2.7/urllib2.py”, line 475, in error return self.\_call\_chain(\*args) File “/usr/lib64/python2.7/urllib2.py”, line 409, in \_call\_chain result = func(\*args) File “/usr/lib64/python2.7/urllib2.py”, line 558, in http\_error\_default raise HTTPError(req.get\_full\_url(), code, msg, hdrs, fp) urllib2.HTTPError: HTTP Error 404: 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:** [April 24, 2019, 6:42pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/6 "2019-04-24T18:42:00Z")
Hi - You are using the version from the Test ToolShed. Tools there are for development (only) and can present with many problems. You’ll need to either consider using the original Kraken tools/DM or wait for the Kraken2 DM to be ready. I don’t have an issue ticket yet for you to track but will check or create one and link it back. I’ll also ping the developer at Gitter to see if they have any advice. They may post back here or at Gitter. Feel free to jump into the conversation either place. [https://gitter.im/galaxy-iuc/iuc?at=5cc0add23b6cb0686a484480](https://gitter.im/galaxy-iuc/iuc?at=5cc0add23b6cb0686a484480) ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 24, 2019, 8:48pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/7 "2019-04-24T20:48:23Z")
Hi @JayanthiG, the kraken2 data manager is a work-in-progress. When it’s complete, it will be uploaded to the main toolshed under ownership of the `iuc` (Intergalactic Utilities Commission) group. My progress on the data manager can be viewed on this pull request: > There is one thing that I could try in the short-term, though I’m not sure that it would solve your issue. I’m not sure that I’ve pushed the latest version of the data manager to the test toolshed. I’ll do that, then you could try re-installing the latest version to see if it works (unfortunately I can’t promise that it will). ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 24, 2019, 8:57pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/8 "2019-04-24T20:57:09Z")
@JayanthiG I’ve attempted to update the test toolshed but it appears that it is already up-to-date. The latest revision is `29:65cbfb5e6f65` from `2019-03-29`. Based on your error message, it looks like the URL that was being used to download the minikraken database is invalid. I’ve just looked at the kraken2 site and it looks like they’ve re-organized the download links for the minikraken db recently (around 2019-04-23): [https://ccb.jhu.edu/software/kraken2/downloads.shtml](https://ccb.jhu.edu/software/kraken2/downloads.shtml) I’ll need to update the data manager to use the new links. The best way to stay up-to-date on the state of this tool is to watch the GitHub pull-request I linked to above. ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 9:13pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/9 "2019-04-24T21:13:27Z")
Great!. Thanks so much. ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 9:20pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/10 "2019-04-24T21:20:12Z")
Thanks Dan. ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 24, 2019, 9:57pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/11 "2019-04-24T21:57:34Z")
@JayanthiG I’ve updated the URL in the data manager and pushed the update to both my GitHub pull-request and to the Test Toolshed. The latest revision ([30:0aaff8fb824d](https://testtoolshed.g2.bx.psu.edu/repository/view_changelog?id=1e2892d26c9e9e05)) should pull the minikraken2 database from the correct location now. ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 10:12pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/12 "2019-04-24T22:12:35Z")
Thanks so much Dan. Appreciate your help on it!. Jayanthi ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 10:31pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/13 "2019-04-24T22:31:20Z")
Hi Dan, Please check the NCBI paths also corrected in the data manager to download the bacterial and viral databases via kraken2. Fatal error: Exit code 1 () Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/bin/kraken2 line 16. Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/bin/kraken2-build line 15. Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/libexec/kraken2-build line 15. Downloading nucleotide est accession to taxon map…rsync: link\_stat “/taxonomy/accession2taxid/nucl\_est.accession2taxid.gz” (in pub) failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1650) [Receiver=3.1.2] Traceback (most recent call last): File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_standard.py”, line 113, in main() File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_standard.py”, line 106, in main target\_directory, File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_standard.py”, line 47, in kraken2\_build\_standard subprocess.check\_call([‘kraken2-build’] + args, cwd=target\_directory) File “/usr/lib64/python2.7/subprocess.py”, line 542, in check\_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ‘[‘kraken2-build’, ‘–threads’, ‘1’, ‘–standard’, ‘–kmer-len’, ‘35’, ‘–minimizer-len’, ‘31’, ‘–minimizer-spaces’, ‘6’, ‘–db’, ‘2019-04-24T222820Z\_standard\_kmer-len35\_minimizer-len31\_minimizer-spaces6’]’ returned non-zero exit status 23 Thanks, Jayanthi ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 24, 2019, 10:37pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/14 "2019-04-24T22:37:11Z")
Hmm, thanks for reporting, but that may need to be fixed in `kraken2` itself. The ‘standard’ data manager works a bit differently. It launches `kraken2-build --standard`, which handles finding and downloading the data from NCBI. So if there is a problem with those URLs it will need to be fixed in the `kraken2` codebase. I’ll try running `kraken2-build` directly on the command-line and see if that has the same problem. ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 24, 2019, 10:41pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/15 "2019-04-24T22:41:45Z")
@JayanthiG It looks like this issue has been fixed in a recent commit: > …but there hasn’t been a `kraken2` release since that commit, so the fixed version isn’t available on bioconda or galaxy. ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 10:56pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/16 "2019-04-24T22:56:54Z")
Dan, I have tried to install it with the latest revision. But it gives me the error. Jayanthi ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 24, 2019, 10:59pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/17 "2019-04-24T22:59:17Z")
@JayanthiG which error are you referring to this time? Which database are you trying to build? ---
**Author:** ![JayanthiG](https://avatars.discourse-cdn.com/v4/letter/j/9fc348/32.png) [@JayanthiG](https://help.galaxyproject.org/u/JayanthiG)\ **Post date:** [April 24, 2019, 11:14pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/18 "2019-04-24T23:14:27Z")
I am trying to download NCBI databases through data manger using **Kraken2 Standard Database Builder** database builder (Galaxy Version 2.0.7\_beta) An error occured while running the tool **testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/kraken2\_build\_standard/2.0.7\_beta**. Tool execution generated the following messages: Fatal error: Exit code 1 () Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/bin/kraken2 line 16. Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/bin/kraken2-build line 15. Possible unintended interpolation of @2 in string at /dep/\_conda/envs/\_\_kraken2@2.0.7\_beta/libexec/kraken2-build line 15. Downloading nucleotide est accession to taxon map…rsync: link\_stat “/taxonomy/accession2taxid/nucl\_est.accession2taxid.gz” (in pub) failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1650) [Receiver=3.1.2] Traceback (most recent call last): File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_standard.py”, line 113, in main() File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_standard.py”, line 106, in main target\_directory, File “/data/shed\_tools/testtoolshed.g2.bx.psu.edu/repos/dfornika/data\_manager\_build\_kraken2\_database/65cbfb5e6f65/data\_manager\_build\_kraken2\_database/data\_manager/kraken2\_build\_standard.py”, line 47, in kraken2\_build\_standard subprocess.check\_call([‘kraken2-build’] + args, cwd=target\_directory) File “/usr/lib64/python2.7/subprocess.py”, line 542, in check\_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ‘[‘kraken2-build’, ‘–threads’, ‘1’, ‘–standard’, ‘–kmer-len’, ‘35’, ‘–minimizer-len’, ‘31’, ‘–minimizer-spaces’, ‘6’, ‘–db’, ‘2019-04-24T222820Z\_standard\_kmer-len35\_minimizer-len31\_minimizer-spaces6’]’ returned non-zero exit status 23 ---
**Author:** ![dfornika](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dfornika/32/275_2.png) [@dfornika](https://help.galaxyproject.org/u/dfornika)\ **Post date:** [April 25, 2019, 12:22am UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/19 "2019-04-25T00:22:24Z")
@JayanthiG Yes, that is out of my control. There will have to be a new release of `kraken2` in order for that functionality to be fixed. There was a recent request on the `kraken2` GitHub issue tracker to tag a new release but it will be up to the maintainers of that repository to decide when to tag the next release @JayanthiG Yes, that is out of my control. There will have to be a new release of `kraken2` in order for that functionality to be fixed. There was a recent request on the `kraken2` GitHub issue tracker to tag a new release but it will be up to the maintainers of that repository to decide when to tag the next release Edit: `kraken2-2.0.8-beta` has been released. Once it’s been updated in bioconda then the galaxy tool can be update to use the latest version. ---
**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:** [April 25, 2019, 6:00pm UTC](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137/21 "2019-04-25T18:00:05Z")
Split this topic on April 25, 2019, 6:00pm UTC 2 posts were split to a new topic: [Kraken2 tool error](https://help.galaxyproject.org/t/kraken2-tool-error/1180) [Next page](https://help.galaxyproject.org/t/how-to-view-kraken2-results-in-krona/1137.md?page=2)