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Revision as of 18:02, 7 December 2014
, 18:02, 7 December 2014→Run GotCloud Align
Now that we have all of our input files, we need just a simple command to run them
Now that we have all of our input files, we need just a simple command to run them
* When running at home if you don't have 4 CPUs, reduce the <code>--numjobs</code> setting (it will take longer to run).
${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numjobs 4 --base_prefix ${SS} --outdir ${OUT}
${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numjobs 4 --base_prefix ${SS} --outdir ${OUT}
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
[[File:gcalignStartNew.png|850px]]
[[File:gcalignStartNew.png|650px]]
This should take 1-3 minutes to run.
This should take about 1 minute to run.
It should end with a line like: <code>Processing finished in 47 secs with no errors reported</code>
It should end with a line like: <code>Processing finished in 54 secs with no errors reported</code>
* The <code>WARNING</code> messages are just to let you know that the default Read Group field settings are being used.
* The <code>WARNING</code> messages are just to let you know that the default Read Group field settings are being used.
