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, 01:17, 15 June 2014
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| 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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| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | Curious if it started running properly? Check out this screenshot: |
| + | <div class="mw-collapsible-content"> |
| + | [[File:SnpcallStart.png|750px]] |
| + | </div> |
| + | </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> |
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| 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. |