Migrate-n is a bioinformatics and population genetics program which is designed to model population sizes, gene flow between populations and past migration rates.
Using Migrate-n on RCC Resources
Migrate-n requires the gnu module to be loaded. Note that there are two versions of the program. These can be called from the command line using the following commands:
# Load the GNU module (for all versions) module load gnu # Load the OpenMPI module (if using parallel Migrate) module load openmpi # Version 3.6.11 migrate-n # Serial migrate-n-mpi # Parallel # Version 4.4.0 migrate-n-4 # Serial migrate-n-4-mpi # Parallel
To run this program in serial, first make a folder in your home directory and make a file named `infile`.
mkdir ~/migrate-n touch ~/migrate-n/infile
Now, copy this example sequence data from the documentation into `infile`:
2 2 Make believe data set using simulated data (2 loci) 50 46 3 3 pop1 eis ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC zwo ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC drue ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC eis ACGCGGCGCGCGAACGAAGACCAAATCTTCTTGATCCCCAAGTGTC zwo ACGCGGCGCGAGAACGAAGACCAAATCTTCTTGATCCCCAAGTGTC drue ACGCGGCGCGAGAACGAAGACCAAATCTTCTTGATCCCCAAGTGTC 2 pop2 vier CAGCGCGCGTATCGCCCCATGTGGTTCGGCCAAAGAATGGTAGAGCGGAG fuef CAGCGCGAGTCTCGCCCCATGGGGTTAGGCCAAATAATGTTAGAGCGGCA vier TCGACTAGATCTGCAGCACATACGAGGGTCATGCGTCCCAGATGTG fuefLoc2 TCGACTAGATATGCAGCAAATACGAGGGGCATGCGTCCCAGATGTG
While in the `migrate-n` directory, execute the program using `migrate-n`.
cd ~/migrate-n migrate-n
A menu will appear, which can be ignored for the purposes of this example. Simply type Y and allow the program to run. The above example will not yield any useful results, but will complete.
Migrate is available with both gnu-openmpi and gnu-mvapich2. Load the desired module before using the package. Running in parallel is identical to running in serial, but instead using `srun -n n migrate-n-mpi` instead of `migrate-n`. The design of this program requires one director node in addition to worker nodes, so for a 4 node job one would require n=5 total nodes.