marbl/krona

Interactively explore metagenomes and more from a web browser.

krona's Issues

New to Krona, Having Trouble Generating Chart from previous OTU table

Hello, I am not much of a computer person, so I cannot figure out what I'm doing wrong. I have an OTU table consisting of the number of OTUs and the phylogeny. When I import the file (which I have attached an example here; columns are [# of OTUs, Kingdom, Phylum, Class, Order, Family, Genus, Species]) using Krona tools, an issue arises and the chart just says 100% unclassified (picture attached). I'm sure it's most likely my input file, but I have no idea how to approach the issue. Thank you for any help you may provide!

test1kronastudy1.txt

Unrecognized escape \A passed through at KronaTools.pm line 1703.

Hi,

I ran into an warning message as title and looking at code source. It looks like there is a spurious backslash @ line 1703 of version 2.6 ( line 1921 of version 2.7).

 $summaryText = " ${memberTag}\All=\"members\"";

Regards,
Chienchi

Unassigned no hits?

I am providing Krona at file with two columns (a query id and an NCBI taxonomy ID). For example:

query1     543  
query2     1  
query3     0  

My call to Krona version 2.6 is: ktImportTaxonomy -i -k -o krona.html and my resulting pie charts would assign query1 to taxonID 543, query2 to "unassigned root" and query3 to "unassigned root" but give me a warning in the terminal that "0" is an unrecognized taxonomy ID and those queries were added to the "unassigned root" group. This produces two wedges.

Instead, I would like to see three wedges, one for 543, one for unassigned root, and one for "no hits" or "unclassified" or something like that. How can I do this? I don't want all my "0" taxonomy IDs to be added into the "unassigned root" group.

Thanks for any help!

Formatting for ImportText.pl ?

Perhaps I'm misunderstanding the directions posted in the wiki on this, but when I import text like the attached, I do not get the same type of output as the example (nutritional information). See attached the text file and the output html file.
Any suggestions on how I'm improperly formatting?

Command:
perl ImportText.pl DNA_krona.txt

DNA_krona.txt

Coloring by categorical attribute & Krona 2.0 XML Specification

The 2011 Ondov et al. BMC Bioinformatics paper says, For categorical variables, users may define the color of every node in the XML, but it's not clear how to express that in the xml file.

The Krona 2.0 XML Specification describes color gradients but there's no mention of discrete colors for categorical attributes.

Thanks very much for any info.

Charts with root only fail to render

If a chart only contains a single level with no children, it will render the UI but no chart and produce JavaScript errors.

Is it possible to visualize a Qiime 1.9 OTU biom file

I've used qiime to generate an OTU table for my datasets. Is it possible to viz with Krona

Taxonomy location variable

Would it be possible to add a check for an environment variable, say $KT_TAXONOMY, and use that to set the location of the taxonomy files? Perhaps a command line option instead or in addition? There are cases where in a shared environment, it is better to have your own taxonomy files and it is difficult/undesirable to update the taxonomy for all users/all cases.

Trademark issue remains preventing distribution by Debian

Hello,

Issue #15 was closed but the issue remains: Ftpmaster refuses the distribution by Debian since we can not provide security fixes.

It would be great if you could drop this trademark restriction.

Kind regards

      Andreas.

No such file or directory at /usr/local/bin/ktImportText line 71

Hello,
I am getting the error of 'No such file or directory at /usr/local/bin/ktImportText line 71'...
I am trying to use krona for my Qiime output. How can I solve the problem.

Thanks,
Selin

Is it possible to hide the percentage

Is it possible to show the last level without its percentage?

Excel template samples number

Hi,
i'm tryng to use the excel Krona template but I can't add new samples columns, what can this be done?

<color ... /> with empty xml element doesn't render

Hello,

This is a minor item that could be fixed in the doc or code.

I'm using python xml.etree.ElementTree to generate Krona xml. ET detected that <color ...> has an empty element and appropriately generated <color ... />. That empty element prevents Krona from rendering.

To see the issue, edit the Example Krona Chart and replace the existing <color ...></color. with:

<color attribute="grams" valueStart="0" valueEnd="55" hueStart="120" hueEnd="240"/>

Thanks very much.

Excel Template to compare 4 datasets?

Hi everybody,

is there an Excel template or a way to expand the Excel template (v2.4) easily to 4 datasets? I want to compare 4 different samples (taxa composition) and use them as figures for my thesis. If I create the charts for each dataset separatly, the taxa have different colors (dependent on the abundance) and it is confusing when I switch between the samples.

Thank you!
Best regards

Support accession to taxonomy mapping

Dear developers,

Thanks for the great tool. We are using you beautiful and useful tool to display taxonomy classification result. Since NCBI is phasing out sequence GIs( use Accession.Version instead, https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/ ),do you have any plan to support this transition?

Regards,
Chienchi

Cannot use Krona

Hi
I've installed excel 97 on my PC, and already run for several times the install_Windows VBScript, but it does not do any thing. I've also installed office 2016 in my PC, could this be interfering? (but I cannot work with out it...).
Can any one help me? I've tried to import/had data to the template Krona.excel to see if I could produce some thing but, I just cannot make it work, and I really wanted to produce Krona graphics from metagenomic data from several samples, all in the same file.
Thank you for any help.
kind regards
Igor

Installation with prefix

Dear Krona authors,
I want to perform local installation of krona on a linux cluster.
so I perform :
./install.pl --prefix /my/path/
But, the program ktImportText doesn't work in that configuration
./ktImportText table.txt
Writing text.krona.html...
Can't read file '/../src/krona-2.0.js' [Aucun fichier ou dossier de ce type]
Please fix it !

now, on windows, I can not open the HTML file, Why?

Too many query IDs to store in chart?

When running krona with ktImportNLAST, I get the following warning: Too many query IDs to store in chart; storing supplemental files in 'blast.krona.html.files'. How can I resolve this issue?

updateTaxonomy.sh errors

Hi,
I have been trying to install KronaTools 2.6.1 in our cluster and I find some errors when running updateTaxonomy.sh.

So, KronaTools after extraction is at /srv/scratch/z3382651/KronaTools-2.6.1, I enter in the folder and install it with no error at all. I tried:
./install.pl --prefix /srv/scratch/z3382651/KronaTools-2.6.1
./install.pl --prefix /srv/scratch/z3382651/KronaTools-2.6.1 --taxonomy /srv/scratch/z3382651/KronaTools-2.6.1/taxonomy/

So far, so good. But when running updateTaxonomy.sh, I get the following error:

/updateTaxonomy.sh: line 115: cd: /srv/scratch/z3382651/metannotate/included_software/KronaTools-2.5/lib/../taxonomy: No such file or directory

Update failed.
Could not enter '/srv/scratch/z3382651/metannotate/included_software/KronaTools-2.5/lib/../taxonomy'. Did you run install.pl?

I could make the updateTaxonomy.sh by doing ./updateTaxonomy.sh taxonomy but I get another error:

./updateTaxonomy.sh: line 99: ktGetLibPath: command not found

Afterwards starts updating though, but I'm not sure if it's going to be ok. I'm installing Krona as dependency of GraftM

Any way to test the installation?

Thanks

NCBI is phasing out sequence GIs

Just curious -- Will NCBI's announcement (announced March last year) affect any Krona functionality? I was under the impression that the taxanomic db that Krona builds (with updateTaxonomy.sh) is keyed off of gi numbers (not accession.version).

https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/

cp: directory Library/Application Support/Microsoft/Office/User Templates/My Templates does not exist

Tax4fun output visualization

Hello,

I have used tax4fun to predicts the functional capabilities of my microbial
communities on 16S data samples.
It gives a output file as . txt and below how it looks like:

Can I use Krona to visualize these data ? I have no idea how to convert the tax4fun output file that can be readable by krona.

Thanks, any help is appreciated,
Selin

Failed to create directory

$ ./updateAccessions.sh
mkdir: cannot create directory `/scratch/godlovedc/Krona/Krona/KronaTools/taxonomy/accession2taxid': No such file or directory

Update failed.
   Could not create '/scratch/godlovedc/Krona/Krona/KronaTools/taxonomy/accession2taxid'. Do you have permission?

ktImportText- multiple samples-one text file

Hi Folks,

I was wondering is it possible to use ktImportText on multiple samples in just one text file?
I have a text file containing multiple samples (actually 20) with taxonomy classification and respective abundances. I could not figure out how to use ktImportText option on this one.
Otherwise, I will have to subset the text file into 20 new files to produce the desired Krona graph. Just want to save some time if possible.

Regards,
Deni

no manual

can't find any usage documents

Help please! Trying to create a Krona chart for the metagenomic analysis of a hot spring

Hi, if someone could help walk me through this I would be ETERNALLY grateful.

I downloaded KronaTools-2.7 as well as the KronaExcelTemplate.

When I tried to instal it (using install_Mac_all_users and install_Mac) I immediately come up with this error message:
“install_Mac_all_users” is damaged and can’t be opened. You should move it to the Trash.

I did try to play around with the example excel template but I am not sure where to begin with this.

I have 1200 OTUs that I would like to incorporate, I am sure that no other schmuck is doing it manually so I came here to ask for help :/

I am not sure where to go from here.. Unfortunately I am not the most computer savvy individual, if there is a relatively straight forward way to do this I would super super appreciate some direction.

Thanks!!

UTF-8 encoding

I'm trying to load the results from Krona as part of my Shiny (R) app. Shiny requires utf-8 encoding. The charset in the HTML from Krona is defined as utf-8, but it wont load into Shiny. If i save the HTML with utf-8 encoding from a text editor, it works fine. Is there a way to ensure encoding when using the excel template?

Option to output svg directly rather than interactive html

This would be a nice feature for those who wish to use Krona's output in automated systems :)

javascript errors on chrome

Frequently we see errors as shown in the attachment on chrome. It looks like the node isn;t defined when it is used or something?
krona-error-1449576408539.log.txt

Trademark restrictions permit distribution by Debian

Hello,

I'm a member of the Debian Med team which is a subgroup of Debian to package free software in life sciences and medicine for official Debian. I created a Debian package of Krona since it is used in another package we intend to provide.

Unfortunately the Debian ftpmaster has rejected the package due to the trademark restrictions. I wonder whether you might consider relaxing this restriction to enable me a simple solution for packaging. Since I only needed to adapt the install.pl script I could avoid the patch by rewriting the install procedure but this might mean extra work for no real profit.

BTW, if you checkout the patch I also fixed a spelling mistake (second chunk of the patch) you might like to take over.

If you might want to stick to the trademark restrictions I could also provide a patch for the install script which takes an optional argument to override $scriptPath. Please let me know what you might prefer.

Kind regards

     Andreas.

KronaExcelTemplate Error - Categories do not merge

Hi,

I ran into some trouble while trying to use the KronaExcelTemplate in Excel v15.32 (2017) on MacOS: the categories do not merge when generating the graph, e.g., using the granola example data without any editing, I get three "Fats" (and three "Carbohydrates") categories, each followed by the subsequent subcategories, rather than a single "Fats" category subdivided into Saturated, Unsaturated, and so on.

I can get the correct graph by importing the data from txt with KronaTools, but the "colouring" according to an additional variable is essential for my purpose. I have not been able to convert my data to xml so far, as I am not really familiar with the format.
Is it possible to fix the graph generation using KronaExcelTemplate and/or import score data from txt?
Ideally, I would like to have a single chart with several (approx. 10) "samples", each with an additional "score" colouring option - is it possible to do this without writing an xml file?

Thanks in advance

Include option to display title on charts

Along with the other chart display options, it would be helpful to be able to pass in a chart title to be displayed above the plot.

FTP is insecure and should be deprecated

Can the taxonomies be moved somewhere more contemporary?

As a hospital, and given current situation with security, our IT team has decided that ftp will be permanently blocked without exception. It's annoying, but they aren't wrong.

KtImportBLAST and some accession numbers.

Hello,

We are using Kronatools to visualise a large number of blasted sequences.
Recently when using the ktImportBLAST module, we receive a warning that says that some accessions are not in a valid format and thus ignored. These are some examples of the accessions that generate this warning:
2AYV_A P0C9A6.1 Q53RJ5.1 3SQ2_A 2X9I_A 2X5G_A 3NE6_A A4WGV2.1 2XEE_A 2UYH_A P0C9B9.1 2OXQ_A 3HXL_A

The weird thing is that these are genuine protein accessions.

Is there a way to make sure that this kind of acession numbers are not ignored?

Thanks in advance.

Krona chart only shows 100% bacteria

Hello all,

I have a blastn file conatining 16s blastn results, and almost half of them are classified by Kona as "unassigned" while it's clear they should be assigned. Now, that file contains several different samples, say samples from "site1" "site2", etc ... and I wanted to focus on each specific sample. So I extracted the blast output for only "site1", for example, and now, Krona only shows a full circle "100% bacteria" with no other taxonomic assignment. However the blast result have well-defined taxonomic assignments.
I did the 2 updates of Accession and Taxonomu

I am not sure to understand Krona behaviour, what am I missing?
Thanks a lot

get list of currently displayed taxonIds

Hi,

Is it possible to retrieve the list of currently displayed taxonIds? I looked in the wiki but couldn't find anything about this...
If this is not possible yet and if your interested in this feature, I can submit a PR to implement it!

thanks in advance

Count link timeout

After opening the html file, clicking on the link for the count times out. This occurs even with a count of 1. The program created a folder as the data was a large set.

Hide collapse checkbox when not applicable

The checkbox in the chart for collapsing redundant wedges is visible and active even when a dataset is not affected by it, which creates interface confusion (noted in #44).

Preferences

I'm wondering if there is a way to have Krona preferences (font size, chart size, etc)? Either when the HTML file is made (e.g., ktImportText --font-size 16 --chart-size +1) or through browser cookies.

Coloring by multiple variables

Parametric coloring in the chart could be selected by a dropdown instead of a checkbox. The XML format would have to be modified to allow multiple <color> tags. Import scripts could utilize this with built in variables (e.g. both e-value and score for BLAST results) or generic columns in text import. The Excel template would be tricker and may need to move to a flexible column model. Suggested in #44.

display to strain level

Hi,
I have some viruses mapped to strain level. While krona successfully grouped the taxID and displayed up to species level, I'm hoping to see the charts displayed in more detail.
Can this be implemented?
Thanks

Problems iwht ktImportBlast with Blastx results and updateAccessions.sh

I get empty html files when using ktImportBlast with Blastx results whereas the same tool works fine with blastn results. I thought it was an accession-list problem and I tried to update accessions with updateAccessions.sh. However, I got an error message:

Sorting dead_nucl.accession2taxid.gz...
Sorting dead_prot.accession2taxid.gz...
Sorting dead_wgs.accession2taxid.gz...
Sorting nucl_est.accession2taxid.gz...
Sorting nucl_gb.accession2taxid.gz...
Sorting nucl_gss.accession2taxid.gz...
Sorting nucl_wgs.accession2taxid.gz...
Sorting prot.accession2taxid.gz...
make: sort: write failed: /tmp/sortpErLfH: No space left on device
*** [prot.accession2taxid.sorted] Error 2

Any idea of what I am doing wrong please?

Changing colors in the chart

I am trying to use kronatools to produce publication-quality figures, but running into a serious issue with the colors. At the first level of taxonomy (archaea, bacteria, or eukarya) the colors are chosen based on abundance (eg the most abundant will become red). But this produces an issue if I am making a figure to compare two populations because now the same group can be colored differently (eg: bacteria labeled red in fig1 but green in fig2) - I need a way to fix this so that the figures can be easily compared.

tldr: I would like to be able to change the colors on the krona chart without resorting to brute force (like paint...).

Thank you!

How to include multiple samples in one chart?

I saw this can be achieved in some examples. But is seems I cannot do that using the Excel template.

Thanks!

Automate export of snapshots

Is there any way to automate (script) the export of snapshot SVG images? Thanks!

Installing Excel template on Mac

I'm receiving an error message when trying to open the downloaded install_Mac file on the Excel Template. It says the file is damaged and can't be opened. Anyone finding similar or have any ideas?

Krona.html is not opening

Krona.html is not opening . I am getting message as :Could not get resources from "http://krona.sourceforge.net".

The same happened 1 week ago. but it was fine after 2 days.
Again the same issue. I would like to get this rectified at the earliest.

"Timed out loading supplemental files..."

Hello,

I am getting the error below when I try to list query IDs per wedge:

"Timed out loading supplemental files for:
file:///path/to/krona_output.html"

I have tried to list the query IDs using Chrome, Firefox and Safari on macOS. Any help would be greatly appreciated.

Krona chart using diamond blast

Hello all,

I am try make Krona chart using blast form diamond. I used the command to DAA output, however, I didn't got convert this file to running in the Krona. Anybody can help me?

Thanks!