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
Serially Running Migrate-n
To run Migrate-n 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 official 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
Navigate to the migrate-n folder and then execute the program using the command 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.
Running Migrate-n in Parallel
Migrate is available with both the gnu-openmpi and gnu-mvapich2 modules. Load the desired module before using the package. Running in parallel is identical to running in serial. To run in parallel, use the command 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, you need n=5 total nodes.
For detailed usage information about Migrate-n, refer to the official documentation.