“Manipulation Environment for Genetic Analyses” A data-handling program for facilitating genetic linkage and association analyses

• https://watson.hgen.pitt.edu/docs/mega2_html/mega2.html

• Module Name: mega2 (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mega2
[user@cn3144 ~]$ mega2 --help
Usage: mega2 [options] [batch-file-name] {arguments}
  acceptable options:
  DB         --DBfile 
                change the database name from dbmega2.db to .
             --DBdump
                dump the database and if --DBread is also present,
                then exec’s a new copy of Mega2 to process the database.
             --DBread
                read an existing database file and do an analysis.
             --DBcompress 
                set database compression level: 0 == off; 1 == gzip; (default == 1).
...
...
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. mega2.sh). For example:

#!/bin/bash
set -e
module load mega2
cd /data/$USER
mega2 command

Submit this job using the Slurm sbatch command.

sbatch --mem=5g mega2.sh

Create a swarmfile (e.g. mega2.swarm). For example:

cd dir1; mega2 command
cd dir2; mega2 command
...
cd dir10; mega2 command

Submit this job using the swarm command.

swarm -f mega2.swarm -g 5 --module mega2