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, 22:57, 18 May 2015
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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: |
− | * When running at home if you don't have 6 CPUs, reduce the --numjobs setting (it will take longer to run). | + | * When running at home if you don't have 8 CPUs, reduce the --numjobs setting (it will take longer to run). |
− | ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} | + | ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} |
| * <code>${GC}/gotcloud</code> runs GotCloud | | * <code>${GC}/gotcloud</code> runs GotCloud |
| * <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline. | | * <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline. |
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| </div> | | </div> |
| </div> | | </div> |
− | This should take about 5-8 minutes to run. | + | This should take about 3-6 minutes to run. |
| * It should end with a line like: <code>Commands finished in 402 secs with no errors reported</code> | | * It should end with a line like: <code>Commands finished in 402 secs with no errors reported</code> |
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