We actually finished a job to completion, with what I believe to be actual results on Hyak! Looking over the output log found here it’s interesting to see a roughly 28x difference between real time and CPU time for read processing, which corresponds to the number of threads I gave the bwa program.
I’m in the process of copying the .sam files up to owl, and when they’re finished in a few hours, they will be found here.
The job submission script is BWARun.sh and gives a good idea of what a Slurm job submission script should look like.
Now back to getting Redundans to work…