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:
- Wang Y, Chen Q, Deng C, Zheng Y and Sun F KmerGO: A Tool to Identify Group-Specific Sequences With k-mers.c Front. Microbiol. 11:2067. doi: 10.3389/fmicb.2020.02067.
Documentation
Important Notes
This application requires a graphical connection using NX
- Module Name: TEMPLATE (see the modules page for more information)
- Multithreaded/singlethreaded/MPI...
- This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
- Environment variables set
- TEMPLATE_HOME
- Example files in ???
- Reference data in /fdb/TEMPLATE/
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 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 |