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?