Chapter 7 Getting phylogenetic markers

7.1 SISRS

Add what SISRS does

In your home folder (cd back there if you need to) type

git clone https://github.com/SchwartzLabURI/SISRS.git to get the software we will use to analyze your data.

Make a new folder for your SISRS results.

Now we need to work with scripts (just like before) to run each step of the analysis. However, this time we’ll take advantage of the computing power of the cluster so that each student in the class can run their analysis on a separate computer. When you log in to Bluewave you are on the “head node”. From here you can submit jobs to run analyses on the other nodes attached to the cluster.

Move into the SISRS folder and then the scripts folder inside that and the slurm_submissions inside that. Slurm is the name of the software used to keep track of all the jobs you submit. Use nano to open 1_submit.slurm. Change the mail user line to your email address. Change the last line to include your data directory and results directory. Also delete the hashtag at the beginning of the line. Exit nano and save the script.

Instead of running the script with the bash command you will submit a job as sbatch 1_submit.slurm. You will get an email when your job is done.

Continue to run steps 2-7 (but not 7a or 7b). You will also need to change the ntasks-per-node line to 20 and use 20 processors any time that information is requested.