MIRA¶
The Mimicking Intelligent Read Assembly (MIRA) application is a multi-pass DNA sequence data assembler and mapper for whole genome projects.
MIRA is available as a module on Apocrita.
Usage¶
To run the default installed version of MIRA, simply load the quast
module:
$ module load mira
$ mira --help
Usage:
mira [options] manifest_file [manifest_file ...]
Options:
-c / --cwd= directory Change working directory
-h / --help Print short help and exit
-m / --mcheck Only check the manifest file, then exit.
-M / --mdcheck Like -m, but also check existence of
data files.
-r / --resume Resume/restart an interrupted assembly
-t / --threads= integer Force number of threads (overrides
equivalent -GE:not manifest entry)
-v / --version Print version and exit
Core Usage
To ensure that MIRA always uses the correct number of cores, the
--threads=${SLURM_NTASKS} option should be used.
Example job¶
Serial job¶
Here is an example job running on 2 cores and 2GB of memory, using an example dataset:
#!/bin/bash
#SBATCH --ntasks=2 # (or -n 2) Request 2 cores
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (2GB total)
#SBATCH --time=1:0:0 # (or -t 1:0:0) Request 1 hour runtime
module load mira
mira --threads=${SLURM_NTASKS} manifest.txt