Command to estimate how long local blastx take to finish the job?

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9.7 years ago

seta ★ 1.9k

Hi everybody,

I'm looking for a command or script to determine how long the local blastx take to finish the job? I access to server with 140 GB of RAM and 32 core and my fasta assembly file is about 46 MB in size, any experience? Your response highly welcomed. Thanks

blast RNA-Seq alignment • 3.2k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by seta ★ 1.9k

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Is your database local? If not and you are accessing different server, they may after some time intentionally delay your queries in order not to overload the server. If local, then good solution would be to take representative sample, run blastx on that and estimate the final time based on these results.

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Biomonika (Noolean) 3.2k

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You might be able to use pv, i've not used it, but seems like it may be able to give you a progress bar and estimate of completion. https://github.com/icetee/pv.

ADD REPLY • link 7.7 years ago by Jon ▴ 360

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