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Old 04-19-2011, 10:09 AM   #1
ercfrtz
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Default BWA in the background

I searched for this but did not find a thread on the subject. I am trying to run BWA in the background. I tried running the command with an ampersand (&) and it didn't work. I tried the following:

command line > output1>&output2 &

And that didn't work. It just ends up starting the job and then stopping. I tried sending the stopped job to the background with bg and it just ended up trying to start the job and then stopping it again.

Is there a way to run a bwa job in the background so I can close the terminal I have open to the server without it killing the job?
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Old 04-19-2011, 10:13 AM   #2
themerlin
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What if you put "nohup" before the command and a "&" after the command? This should let the command run in the background with all screen output directed to nohup.out

-Jason
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Old 04-19-2011, 10:22 AM   #3
ercfrtz
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That just stops the job as well.

Edit:

It looks like this is actually working so far. I will see if I get the output I desire. Thanks.

Last edited by ercfrtz; 04-19-2011 at 11:58 AM. Reason: Clarification
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Old 04-19-2011, 12:51 PM   #4
iansealy
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Alternatively, try using screen. It's extremely useful for this kind of thing.
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Old 04-19-2011, 01:36 PM   #5
Richard Finney
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Default watch your spaces in the command line

Try this:

jobwhatever > output1 2> error2 &

Based on what I can copy/paste from your post, you are writing all output (stdout AND stderr) to one file : output2.
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Old 04-20-2011, 06:46 PM   #6
robs
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The first & sign would only be useful if you want to write the standout and stderr to the same file:

jobwhatever >output1 2>&1 &

Otherwise, Richard's command will do the job.
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Old 04-20-2011, 09:50 PM   #7
lh3
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Quote:
Originally Posted by robs View Post
The first & sign would only be useful if you want to write the standout and stderr to the same file:

jobwhatever >output1 2>&1 &

Otherwise, Richard's command will do the job.
Please don't do this way. For bwa, stdout and stderr must be separated.
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Old 04-21-2011, 09:04 AM   #8
robs
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The comment was meant for the general case and not particularly for BWA (that's why is says "jobwhatever").

I agree that for BWA that is not the command you would want to use.
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