FastME¶
FastME is a distance based phylogeny reconstruction program that works on distance matrices and sequence data.
FastME is available as a module on Apocrita.
Usage¶
To run the default installed version of FastME, simply load the fastme
module:
$ module load fastme
$ fastme --help
fastme [-i input data file] [-u input user tree file]
[-o output tree file] [-O output matrix file] [-I output information file]
[-B output bootstrap trees file] [-a] [-m method] [ -D[model] | -P[model] ]
[-r] [-e] [-g[alpha]] [-n[NNI]] [-s] [-w branch] [-d datasets] [-b replicates]
[-z seed] [-c] [-f] [-T number of threads] [-v] [-V] [-h]
For full usage documentation, run fastme --help.
Core Usage
To ensure that FastME uses the correct number of cores, the -T ${SLURM_NTASKS}
option should be used.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#SBATCH -n 1 # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core
#SBATCH -t 1:0:0 # Request 1 hour runtime
module load fastme
fastme -i input_file.phy \
-o output_tree_file.tree \
-T ${SLURM_NTASKS}