Local BLAST+ search very slow
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5.7 years ago

I am blasting several assembled contigs from IDBA-UD with lengths between 13,000 and 250bp. BLAST+ seems to be taking a very long time to achieve this. I am using a local nt database and the job should have plenty of memory (25Gb). If I take this same file and use the web based BLAST portal it takes under 10 minutes. What explains the extremely slow local speeds? Is there anything I am not configuring properly?

This is being run through SLURM.

blast contig • 2.7k views
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You can't compare the speed of your local hardware with resources that NCBI has.

Is there anything I am not configuring properly?

Probably Few things to check. Are you using multiple threads and asking for appropriate SLURM resources (n=X cores etc) to go with that. You may want to try and replicate the settings on the web blast on local search (to limit number of hits etc).

Breaking up your initial search into multiple files and starting parallel blast jobs would be another option to look into.


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