KmerGO2 on Biowulf

KmerGO KmerGO is a user-friendly tool to identify the group-specific sequences on two groups of high throughput sequencing datasets. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered “group-specific” here. Furthermore, KmerGO can also be applied to capture trait-associated sequences for continuous-trait dataset.

References:

Documentation
Important Notes

This application requires a graphical connection using NX

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive
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 TEMPLATE

[user@cn3144 ~]$  

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load TEMPLATE
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the swarm command.

swarm -f TEMPLATE.swarm [-g #] [-t #] --module TEMPLATE
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module TEMPLATE Loads the TEMPLATE module for each subjob in the swarm