Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Calling Your Own Genome, May 2015 (view source)

Revision as of 11:19, 20 May 2015

1,846 bytes removed ,  11:19, 20 May 2015
no edit summary
Line 7: Line 7:  
</div>
 
</div>
   −
<div class="mw-collapsible" style="width:500px">
+
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
== Tuesday - Start SNP Calling ==
 
== Tuesday - Start SNP Calling ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
Line 102: Line 102:  
</div>
 
</div>
   −
<div class="mw-collapsible mw-collapsed" style="width:500px">
+
<div class="mw-collapsible" style="width:500px">
   −
== Wednesday ==
+
== Thursday ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
   −
<div class="mw-collapsible" style="width:500px">
   
=== Checking if snpcall Completed ===
 
=== Checking if snpcall Completed ===
−
<div class="mw-collapsible-content">
+
==== Resume screen to Check Jobs ====
−
==== Logging Back in to Check Jobs ====
      
;How do you log back into screen?
 
;How do you log back into screen?
 
  screen -r
 
  screen -r
 
This will resume an already running screen.
 
This will resume an already running screen.
 +
 +
Your screen session still has your environment variables set, so you do not need to reset them.
 +
    
Verify you got a "completed successfully" message.
 
Verify you got a "completed successfully" message.
Line 120: Line 121:  
How long did snpcall calling take?  Look at the log message - time in seconds.
 
How long did snpcall calling take?  Look at the log message - time in seconds.
   −
=== Detach From screen===
  −
Detach from screen.  We will resume it again later when we start SNPCall.
  −
Ctrl-a d
  −
  −
</div>
  −
</div>
  −
  −
=== INDEL Tutorial ===
  −
Now we are going to run the INDEL Practical
  −
  −
Please go to: [[SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015]]
  −
  −
We will Start INDEL Calling after the practical.
  −
  −
  −
<div class="mw-collapsible" style="width:500px">
  −
  −
=== Start INDEL Calling ===
  −
<div class="mw-collapsible-content">
  −
==== Resume screen ====
  −
  −
;How do you log back into screen?
  −
screen -r
  −
This will resume an already running screen.
  −
  −
Your screen session still has your environment variables set, so you do not need to reset them.
      
==== List of BAMs ====
 
==== List of BAMs ====
Line 155: Line 130:  
:<code>SampleXX  SampleXX/output/bams/SampleXX.recal.bam</code>
 
:<code>SampleXX  SampleXX/output/bams/SampleXX.recal.bam</code>
 
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 +
    
==== GotCloud INDEL Configuration ====
 
==== GotCloud INDEL Configuration ====
Line 160: Line 136:  
  cat ~/$SAMPLE/gotcloud.conf
 
  cat ~/$SAMPLE/gotcloud.conf
   −
Same as it looked yesterday with no special Configuration settings for INDEL calling.
+
Same as it looked the other day with no special Configuration settings for INDEL calling.
    
==== Running INDEL ====
 
==== Running INDEL ====
−
Run GotCloud indel with 8 jobs running in parallel
+
Run GotCloud indel with 6 jobs running in parallel
−
* Why 8? 
+
  ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 --outdir $OUT
−
** You want to run as many as you can.
  −
** 3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine
  −
  ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 8 --outdir $OUT
   
* Only need the configuration, number of threads, and the output directory, rest is specified within the configuration.
 
* Only need the configuration, number of threads, and the output directory, rest is specified within the configuration.
   Line 187: Line 160:  
</div>
 
</div>
 
</div>
 
</div>
−
</div>
  −
</div>
  −
  −
<div class="mw-collapsible mw-collapsed" style="width:500px">
  −
  −
== Thursday ==
  −
<div class="mw-collapsible-content">
  −
=== Checking if INDEL Completed ===
  −
==== Logging Back in to Check Jobs ====
  −
  −
;How do you log back into screen?
  −
screen -r
  −
This will resume an already running screen.
  −
  −
==== Checking Completion ====
  −
  −
Did you get a "completed successfully" message?
  −
  −
If yes, how long did INDEL calling take?  Look at the log message - time in seconds.
  −
  −
If no, are you running on seqshop-server?  If so, KILL it.  ssh -X to one of the seqshop machines and run on there.
  −
Ctrl-c
  −
  −
Detach from screen.  We will resume it again later.
  −
Ctrl-a d
  −
  −
=== Ancestry Tutorial ===
  −
Now we are going to run the Ancestry Practical
  −
  −
Please go to: [[SeqShop: Estimates of Genetic Ancestry Practical, May 2015]]
  −
  −
  −
==== Log Out ====
  −
;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.
  −
  −
exit PuTTY
  −
  −
   
</div>
 
</div>
 
</div>
 
</div>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13388"

Navigation menu