Tophat Multi-Thread

ECHo · 02-08-2010, 10:24 PM

Hi, I've used the following command:
./tophat -r 5 -p 12 ../bowtie-0.12.1/indexes/chr21 ../bowtie-0.12.1/TestData/s_1_1_sequence.txt ../bowtie-0.12.1/TestData/s_1_2_sequence.txt

-p 12 I think it could use up to 12 core/thread processing
So, I use "top" command to see the system monitor.
However, the bowtie operation, which is called by tophat uses only 100%CPU.
Why not approaching 1200%CPU usage?

Thanks.

ECHo · 02-08-2010, 10:34 PM

kind of weird...
now it shows 1200%CPU

Don't know why?

Cole Trapnell · 02-08-2010, 11:09 PM

This is normal - not all phases of the TopHat run are multi-threaded.

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02-08-2010, 10:24 PM	#1
ECHo Member Location: Taiwan Join Date: Jan 2010 Posts: 17	Tophat Multi-Thread Hi, I've used the following command: ./tophat -r 5 -p 12 ../bowtie-0.12.1/indexes/chr21 ../bowtie-0.12.1/TestData/s_1_1_sequence.txt ../bowtie-0.12.1/TestData/s_1_2_sequence.txt -p 12 I think it could use up to 12 core/thread processing So, I use "top" command to see the system monitor. However, the bowtie operation, which is called by tophat uses only 100%CPU. Why not approaching 1200%CPU usage? Thanks.

02-08-2010, 10:34 PM	#2
ECHo Member Location: Taiwan Join Date: Jan 2010 Posts: 17	kind of weird... now it shows 1200%CPU Don't know why?

02-08-2010, 11:09 PM	#3
Cole Trapnell Senior Member Location: Boston, MA Join Date: Nov 2008 Posts: 212	This is normal - not all phases of the TopHat run are multi-threaded.