Question: Local blast memory usage
1
gravatar for haylogo
2.6 years ago by
haylogo20
haylogo20 wrote:

I just downloaded pre-formated nt database from ncbi and the latest version of blastn. When I try to blast single sequence (with 1427 nucleotids length) blastn just eats all of my RAM (around 95%) and the process takes really really long time (around 20 mins against 3 mins with -remote blast). On my PC I have Windows 7 64x, amd fx-8350 and 8 gb of RAM.

I use these parameters and they looks for me pretty similar to the parameters in default blastn search in the online version of blast. (db="nt", max_target_seqs = 100, task = "blastn", num_threads = 8, outfmt=5)

Can you please explain what am I doing wrong? Or maybe my PC isn't good enough and I should buy more RAM?

blast ram • 1.7k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by haylogo20
2

With nt database you are going to need 20-30G of free RAM to do the search in memory so no it is not you doing something wrong but hardware limits of your PC.

ADD REPLYlink written 2.6 years ago by genomax64k
1

Thank you for your answer. I am working with with cyanobacteria only atm. What should I do - filter original nt database or search for some filtering commands for blastn application?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by haylogo20

If you are only interested in certain class of organisms then you could subset the nt database to just those sequences. Reducing the search space does have implications for e-values you would get.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax64k
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