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Old 02-08-2010, 09:24 PM   #1
ECHo
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Default 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.
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Old 02-08-2010, 09:34 PM   #2
ECHo
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Unhappy

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

Don't know why?
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Old 02-08-2010, 10:09 PM   #3
Cole Trapnell
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Default

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