Question: num_threads with blastn in blast 2.6.0+
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gravatar for navela78
13 months ago by
navela7860
navela7860 wrote:

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.

blast • 618 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by navela7860
1

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

KK

ADD REPLYlink written 13 months ago by karthic100

have you tried it and seen it using multiple cores?

ADD REPLYlink modified 13 months ago • written 13 months ago by navela7860

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

ADD REPLYlink modified 13 months ago • written 13 months ago by karthic100

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.

ADD REPLYlink written 6 weeks ago by jiaobingke20
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