[Bioperl-l] BlastPlus usage inquiry

Ross KK Leung ross at cuhk.edu.hk
Wed Mar 31 17:28:59 EDT 2010

Dear all,

I know it is inappropriate to raise this question in bioperl but as I
received no better response from NCBI and so have to ask in this group
(because finally I'll use bioperl to call blastplus). I have already been
using the latest blastplus (the command is blastn directly) and found the
problem of running slow and inability to run in a parallel/multithread

Previously I was using non blastplus version 2.2.22 with the command
blastall -p blastn -a 8 etc.

With similar arguments as below except the word size was 12, my shell script
for the same input and database finishes almost instantly. I notice that
except word size and min raw gapped score were changed by me, nothing
appears to differ from the previous version parameters. Moreover, when I top
my process, I find it uses only one CPU instead of 7.
What may be the problem for the script that makes the job running for a day
and still hasn't finished?
blastn -query $1 -db $2 -out $1_$2.xml -num_threads 7 -word_size 4 -gapopen
3 -gapextend 1 -penalty -2 -outfmt 5 -xdrop_ungap 30 -xdrop_gap 30
-xdrop_gap_final 30 -min_raw_gapped_score 10

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