My group is setting up to run some metagenomic analyses over the next month or so. This is currently running on the instance firstname.lastname@example.org. The default 4 cores and 32GB RAM work fine for the assembly stages, but we are going to struggle with building adequate databases for classification.
Would it be possible to upgrade the cores/RAM on this instance? I think RAM between 150-200GB and ~32 cores would work great.
Thanks for your help,
What databases do you need to build?
Nick has made a full kraken database of RefSeq as of Nov 2017 available (link in this thread - Full Kraken database). Is that any help?
All the best,
Thanks for getting back to me.
Yep I spotted the kraken build which I have been using. I also intend to use CLARK and kaiju, which need up to 156GB to build and ~60GB to run (in the case of CLARK).
I could probably run the tools okay with the default setup, but is there a way to briefly access more memory for building the databases?
I will pass your request for a high mem VM onto the site admins and get back to you when I have a response.
All the best,
We can give you the ability to launch a larger VM, however only for a little bit.
When you to Bryn to launch a new VM under type, you should now see, g1.48c256r, which lets you launch a VM with 48 core and 256G of ram.
We’ll remove the ability to launch the VM and any VMs launched of this size on the 2nd of November.
Thanks very much for this. This will be plenty of time for us.
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