num_threads with blastn in blast 2.6.0+

Question

[navela78]

Can someone confirm that using the -num_threads option uses multiple cores for blastn in blast2.6.0+? I am unable to get blastn running on multiple cores even for part of the blast process. I am blasting against the nt database.

blastp against nr database uses multiple cores when num_threads is set >1 but not blastn against nt database.

[karthic]

It may not use all the threads allocated by you. However it uses multiple threads according to its requirement.

KK

[navela78]

have you tried it and seen it using multiple cores?

[karthic]

Ofcourse several times.

Here is the sample command..

blastn -query query_sequence.fa -db /blastdb/nr -evalue 0.0001 -outfmt "6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore qcovs" -out blast_output.txt -perc_identity 100.00 -num_threads 5

[jiaobingke]

Yes. The cores specified by -num_threads are not always used in the process. You can look at this link http://voorloopnul.com/blog/how-to-correctly-speed-up-blast-using-num_threads/. When the -num_threads is 4, your can get a good balance between time and resource.