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Running Rnahybrid In Batch

Hi everyone,

I am running RNAhybrid commands for many files using various parameters. I integrated all these RNAhybrid commands in a pipe.sh file and run bash pipe.sh for this task. However, it is low in speed, because it is running RNAhybrid command one afer another. I am wondering how to run these RNAhybrid commands in parallel. Could anyone kindly provide me suggestions and answers? I appreciate your help very much!!

RNAhybrid [parameter 1] input1 > output1
RNAhybrid [parameter 2] input1 > output2
RNAhybrid [parameter 1] input2 > output3
RNAhybrid [parameter 3] input2 > output4
... ...
• 3,108 views • link
updated by Biomonika (Noolean) Biomonika (Noolean) • written by biolab biolab

You may want to take a look at the discussion on SO.

• 37 views • link
written by Zhaorong Zhaorong

Thanks a lot! Really helpful.

• 0 views • link
written by biolab biolab

1 answer

Use the commands you are using but add "&" at the end of each. 

RNAhybrid [parameter 1] input1 > output1 &
RNAhybrid [parameter 2] input1 > output2 &
RNAhybrid [parameter 1] input2 > output3 &
RNAhybrid [parameter 3] input2 > output4 &

However, without studying deeper you may as well end up overloading the server or being unable to kill the unwanted processes. Least you can do is to remember PID (process ID) you get after running these.

• 31 views • link
written by Biomonika (Noolean) Biomonika (Noolean)

Thank you very much! It is really helpful.

• 0 views • link
written by biolab biolab

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