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SeqShop: Calling Your Own Genome, December 2014 (view source)

Revision as of 22:54, 8 December 2014

85 bytes removed ,  22:54, 8 December 2014
→‎Running SnpCall
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== Running SnpCall ==
 
== Running SnpCall ==
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${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
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Run GotCloud snpcall with 6 jobs running in parallel
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* Why 6? 
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** You want to run as many as you can.
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** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
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${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
 
* Only need the configuration & number of threads, rest is specified within the configuration.
 
* Only need the configuration & number of threads, rest is specified within the configuration.
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This will run overnight. We will check if it completed at the practical in the morning.
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Run 4 jobs on our mini-cluster
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  $GC/gotcloud snpcall --conf ~/personal/gotcloud.2x.conf --numjobs 4 --batchtype mosix --batchopts "-j10,11,12,13"
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* --batchtype says to use mosix (our cluster system)
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* --batchopts tells mosix the options to run with
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** for mosix, -j10,11,12,13 says to run on nodes 10, 11, 12, & 13 - the names of the 4 nodes on our mini-cluster
      
== Exome ==
 
== Exome ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12222"

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