Command line BLAST is very slow
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2.2 years ago

Hi Fellow Bioinformaticians,

I'm running command line BLAST on an EC2 instance (r4.8xlarg, 32 cpus and 244 GB memory), and it is super slow. I have limited my search to humans only and used 8 threads. However, it looks like most of the processes are delayed as shown below. The command run here is blastp against the nr database.

enter image description here

I was wondering if you have any suggestions on accelerating the running time?

Thank you very much!

blastp BLAST blast blastn • 1.3k views
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Please post your complete command line. What database are you blasting against and how much RAM is on this instance?

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Details added, thanks!

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Are you using -num_threads option in your command line (which you did not include).

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Sure, num_threads is set to 8 as described in the quesiton.

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Since you have 32 cores available you could have chosen more threads but that will require you to restart the job. It must be proceeding at the fastest pace it can based on your current selections.

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It would also be helpful to post the rest of (h)top screen. Are there any kswapd or kworker lines in it?

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