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Revision as of 01:17, 15 June 2014
, 01:17, 15 June 2014→Run GotCloud SnpCall
Now that we have all of our input files, we need just a simple command to run:
Now that we have all of our input files, we need just a simple command to run:
${GC}/gotcloud snpcall --conf ${GC}/inputs/gotcloud.conf --numjobs 4 --region 22:36000000-37000000
${GC}/gotcloud snpcall --conf ${IN}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000
* --numjobs tells GotCloud how many jobs to run in parallel
* --numjobs tells GotCloud how many jobs to run in parallel
** Depends on your system
** Depends on your system
* --region 22:36000000-37000000
* --region 22:36000000-37000000
** The sample files are just a small region of chromosome 22, so to save time, we tell Gotcloud to ignore the other regions
** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions
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Curious if it started running properly? Check out this screenshot:
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[[File:SnpcallStart.png|750px]]
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</div>
This should take about 5 minutes to run.
This should take about 5 minutes to run.
* After about 4 minutes of running, GotCloud snpcall will output some text to the screen. Don't worry, that is expected and is just output from some of the intermediate tools.
It should end with a line like: <code>TBD</code>
* It should end with a line like: <code>Commands finished in 289 secs with no errors reported</code>
If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
