stoping a TopHat alignment

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7.5 years ago

snp87 ▴ 80

Hi, I'm trying to stop a TopHat alignment (my computer is low in memory and the run is failing to report the final output (it's been stuck at that stage for about 20 hours now and usually the whole alignment would only take around 6 hours). Is there a way I could stop that particular alignment without force quitting the terminal window?

Thank you!

RNA-Seq • 1.2k views

ADD COMMENT • link 7.5 years ago by snp87 ▴ 80

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Did you try ctrl-Z?

ADD REPLY • link 7.5 years ago by Benn 8.3k

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you could do 'top' and then k (to kill a process), write the PID of this tophat and press enter. of course, this should be done from a different terminal window (unless you are using screen)

ADD REPLY • link 7.5 years ago by lm687 ▴ 50

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ps aux | grep -i "tophat"

then it will give you process ID kill -9 "process id from previous step"

Or as suggested above use top or htop find the process (tophat) then kill it using F9

more can be found here

ADD REPLY • link 7.5 years ago by Medhat 9.8k

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