Request for additional cores/RAM


#1

Good morning,

My group is setting up to run some metagenomic analyses over the next month or so. This is currently running on the instance ubuntu@137.44.59.111. 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,
Harry


#2

Hi Harry,

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,
Sion


#3

Hi Sion,

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?

Thanks again,
Harry


#4

Hi Harry,

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,
Sion


#5

Hi @harry.pickering

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,
Imran


#6

Hi Imran,

Thanks very much for this. This will be plenty of time for us.

Much appreciated,
Harry


#7

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