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| | The settings needed for Single Sample SNP calling that we need for tomorrow are already in the gotcloud.conf (requires extra settings as the default snpcall works best for multiple samples). | | The settings needed for Single Sample SNP calling that we need for tomorrow are already in the gotcloud.conf (requires extra settings as the default snpcall works best for multiple samples). |
| | | | |
| − | == Run your Alignment == | + | === Ran the Alignment === |
| | + | It took many threads & a couple of days to get all of the alignments complete - which is why I ran them last week. |
| | + | * Used screen to run overnight. |
| | | | |
| − | === Screen ===
| + | I ran something like: |
| − | The alignment pipeline will run overnight, but you'll want to log out.
| + | gotcloud align --conf gotcloud.conf --numjobs 4 |
| | + | * I set numjobs to the number of samples I was processing on that machine |
| | | | |
| − | ; How do I leave something running on the server even if I log out?
| + | == Alignment Pipeline Output == |
| − | : One solution is screen!
| |
| − | | |
| − | ; How do I use screen?
| |
| − | : Before running your command, you need to start screen:
| |
| − | : <pre>screen</pre>
| |
| − | | |
| − | [[File:Screen.png]]
| |
| − | | |
| − | As it says, press <code>Space</code> or <code>Return</code>.
| |
| − | * It should now look basically the same as your normal command line.
| |
| − | | |
| − | You can now start your alignment:
| |
| − | /home/mktrost/seqshop/gotcloud/gotcloud align --conf ~/personal/gotcloud.2x.conf --numjobs 1
| |
| − | Yes, leave that as /home/mktrost/seqshop/gotcloud/gotcloud - that is where gotcloud is installed. The ~/... points GotCloud to your specific configuration file.
| |
| − | | |
| − | You should now see your alignment running:
| |
| − | | |
| − | ;Want to log out and leave your job running?
| |
| − | In the screen window, type:
| |
| − | Ctrl-a d
| |
| − | (Hold down Ctrl and type 'a', let go of both and type 'd')
| |
| − | * This will "detach" from your screen session while your alignment continues to run.
| |
| − | | |
| − | ;How do you log back into screen tomorrow?
| |
| − | screen -r
| |
| − | This will resume an already running screen.
| |
| − | * Feel free to test it out and you will see your alignment still running
| |
| − | ** Just use Ctrl-a d to detach from screen and leave your job running
| |
| − | | |
| − | ; Scrolling problems?
| |
| − | : If you want to scroll and screen doesn't scroll like you normally would?
| |
| − | :* Type Ctrl-a Esc and you should be able to scroll up with your mouse wheel
| |
| − | :** Or at least that is what I do from my Linux machine - (sorry I'm typing this up/testing these commands from Linux and not windows, so can't test it out)
| |
| − | | |
| − | | |
| − | == Log Out == | |
| − | If you have not detached from screen:
| |
| − | Ctrl-a d
| |
| − | | |
| − | exit PuTTY
| |
| | | | |
| | == FEEDBACK! == | | == FEEDBACK! == |
| − | Since I didn't send this out yesterday, today's survey has feedback for Tuesday & Wednesday.
| + | Please provide feedback on the lectures/tutorials from today. |
| − | https://docs.google.com/forms/d/1qaLHq9w1Ib3FZq0CtlrbK_-breNiqGRV06oRYNmUuME/viewform
| |
