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Also note that bwa writes its (binary) output to standard output by default, so we need to redirect that to a .sai file.

We will execute these commands directly (not in a batch job), but since they are fairly large files we will first set up an interactive development (idev) session, which will give us a compute node for 3 hours:

Code Block
titleStart an idev session
idev -p normal -m 180 -N 1 -n 24 -A UT-2015-05-18 --reservation=CCBB