I’m trying to use krona pie chart but each time I’m getting an error and it says I need to allocate more memory or size the file down or that I should use a different tool.
\If anyone has some insights or some way that I could make this work or go in another direction that would be super helpful!! If you need to know anything else, I would love to let you know
Please post your Galaxy history so we can further examine. Thanks.
Just would like to also see how big is your dataset and if too large, I would just get a more manageable subset (subsample) to work with.
Here’s my galaxy history
Hey Paige,
I checked out your history and I don’t think it’s a memory issue - Krakentools needs a Kraken report file to convert to Krona, so all you need to do is run Kraken again and turn on the toggle at the bottom for creating a report.
So it goes:
Kraken2 → Krakentools on Kraken Report (not classification) → Krona on Krakentools output.
Also just a note, assuming this is a short read pair, you might try using Bowtie2 for mapping host genomes. Minimap2 is aimed at long reads (I think) and produced worse results for me.
Good luck!
Yes, exactly. Please see this previous forum conversation for more info on how to generate the right input files for Krona.
Thank you so much I was having a hard time but I’ll try that now and see how that goes.
