Blastx only uses one thread when word size is above 3
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11 months ago

Hi all,

I'm using blast version 2.12.0 and running the following command

blastx -db my_db -query ecoli.fna -num_threads 8 -word_size 3

The query runs pretty fast and if I check the CPU usage is always around 600-700%. However, if I increase the word size to 4 or more, CPU usage is always 100%, and the query takes much longer. The same thing happens if I run:

blastx -db my_db -query ecoli.fna -num_threads 8 -task blastx-fast

Is it not possible to increase the word size and run a multi-thread query at the same time?

Thanks!

blastx blast • 361 views
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Hi Guzman, I see a similar pattern. Did you find the reason for this behavior or a solution?

Best, Henrietta

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