blast2go command line!

[PSW]

Hello friends,

I am a new user of blast2go pipeline.

I would like to use blast2go pipeline to obtain annotation for a blast output file which is about 17 Megabytes in size. I did blast against nr seperately and I have the output as *.xml file from my blast. We have a 16 core linux machine and I would like to run blast2go pipeline in that linux machine.

I am not sure if there is an option for setting the number of threads while running blast2go pipeline.

The b2g4pipe command that I used on linux command line to test a small sample blast output is

nohup java -Xmx1000m -cp *:ext/*: es.blast2go.prog.B2GAnnotPipe -in 10_BlastResults_2011.xml -out b2gpout -prop b2gPipe.properties -annot &

It works fine and I could get the output without any problem.

For running b2g4pipe on a larger blast output file in xml format:

Could you please let me know if I could set the number of threads(no of cores/cpu's) in the above b2g4pipe command( like how we do in blastx command line with -num_threads option) to make the annotation process faster? If not, then is there any other way to do it?


Thanks very much.

Cheers,
PSW.

[maubp]

The best way to speed up Blast2Go or b2g4pipe is to setup a local Blast2GO database rather than connecting to their public database in Spain.