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.
This application requires a graphical connection using NX
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 ~]$
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
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 TEMPLATEwhere
|-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|