Blastx only uses one thread when word size is above 3

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

• 1,122 views • link

updated 4.7 years ago by HenriettaHolze •

• written 4.8 years ago by guzmanvigliecca •

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

Best, Henrietta

• 0 views • link

written 4.7 years ago by HenriettaHolze •

0 answers

No answers yet.

More posts like this

How to set the number of mismatch in blastn
written 5.1 years ago by jahanshahi.amin •

Hi everyone, I'm running blast nucleotide with word-size of 6 using the following command: blastn -query 6452.fasta -db ref -out BlastResults.txt -num_threads 8 -outfmt '6 …
Blastx against nr for plants
written 5.8 years ago by m.s_tabatabaei •

Hi every one, I run the Blastx aginst nr using this commend line " blastx -db blastdb_Nr/Blast_Nr -query Query -taxidlist 33090.txids -evalue 1.0e-5 -num_threads 23 …
Blastn .XML to FASTA
written 7.0 years ago by baurumon •

I have run this command: blastn -query work.fa -task blastn -db nr -out out.XML -outfmt 5 -evalue 1e-10 -word_size 4 -num_alignments 1 -num_threads 15 ![enter …
trying to reproduce mirbase blastn
written 8.4 years ago by shinken123

Hi I am trying to reproduce blastn results from the mirbase webpage. Using this: blastn -query query -db db -max_target_seqs 100 -reward 5 -penalty -4 …
Blast results only print to terminal
written 8.6 years ago by darzenis •

I am trying to run blastx using the command below, but the output is not a separate file – the results only print to my …
standalone blastp: increasing word size extremely slows down the search
written 9.0 years ago by aleksanderczeszyk •

Hello, I need to blastp a genome (15,000 seqs) against genome (12,000 seqs) using Biopython. I decided to use local blast and query genome 1 …
blastx threading causing error
written 10.3 years ago by uriamo •

Hey, I'm using blast 2.2.28 and a local db (on a cluster). Whenever I tried to use multiple threads in order to speed up things …
blastx generates empty output file
written 10.4 years ago by dovi

I am trying to run blastx (version 2.2.28) with the following command line: blastx -db nr -outfmt 5 -evalue 1e-3 -word_size 3 -show_gis -num_alignments 1 …
BLAST options error: tried to set option (130) and value (1), line (537)
written 11.2 years ago by oliver.bayfield •

I'm running local blast/2.2.30+ (on a server), command blastx (`-task blastx-fast`) against the nr database, with a query file of about 2000 fasta nt sequences …
For Loop Is Not Working Within My Script
written 13.4 years ago by federico.gaiti

Hi all I made a script in bash that run blastx. ``` #!/bin/sh -l # $Id: Barrine.sh federicogaiti $ echo "Right now it is:" date …