BWA in the background

[ercfrtz]

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?

[themerlin]

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

[ercfrtz]

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.

[iansealy]

Alternatively, try using screen. It's extremely useful for this kind of thing.

[Richard Finney]

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.

[robs]

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.

[lh3]

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.

[robs]

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.