Hello! I have a file “stability.trim.contigs.good.unique.nr_v138_1.wang.tax.summary” created through SILVA database reference. I know KronaTools doesn’t work with Mothur files directly, though I’ve poked around and found Python scripts that convert tax.summary file into XML file that can be then used to create piechart using KRONA.
However, when I approach the step where you put a command: “mothur_krona_XML.py /path/to/tax.summary > output.xml”
I do get incomplete output.xml file that looks something like this:
While it is supposed to look something like this [that’s an example for a serving of granola though…):
http://krona.sourceforge.net/examples/xml.txt
As you can see, just a small part of the “tax.summary” file was converted.
How do I fix that? Is the script outdated or am I just doing something wrong? Maybe there’s some other, simpler way to achieve the Krona piechart?
Help would be very much appreciated, thanks in advance!
