Speed up psiblast of 11k alignments

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4.9 years ago

fhsantanna ▴ 610

I have 11,000 protein alignments and I have to blast each one to 20,000 bacterial genomes using psiblast. How could I speed up this process? Is it possible using more than one computer for it using gnu parallel? Thanks.

psiblast parallel • 1.6k views

ADD COMMENT • link updated 4.8 years ago by Biostar 20 • written 4.9 years ago by fhsantanna ▴ 610

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Is it possible using more than one computer for it using gnu parallel?

https://www.gnu.org/software/parallel/parallel_tutorial.html#Remote-execution

ADD REPLY • link 4.9 years ago by WouterDeCoster 47k

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For this purpose, how do I share the database? Does the host do it automatically?

ADD REPLY • link 4.9 years ago by fhsantanna ▴ 610

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I have no idea, and I've never done anything like this.

ADD REPLY • link 4.9 years ago by WouterDeCoster 47k

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check the --transfer option in the link above.

ADD REPLY • link 4.8 years ago by Jean-Karim Heriche 27k

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What kind of compute resources do you have access to?

ADD REPLY • link 4.8 years ago by Jean-Karim Heriche 27k

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At the time of posting the question, I had three Desktop computers having 20 threads in total (4, 8, and 8 threads). Fortunately, after that, we bought another pc with SSD HD and 16 threads, and I managed to do all blasts using parallel in one week, using only this new computer.

ADD REPLY • link 4.8 years ago by fhsantanna ▴ 610

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