RagTag on Biowulf

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.

Tasks include:

Ragtag also provides command line utilities for working with common genome assembly file formats.


Important Notes

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 ragtag

[user@cn3144 ~]$ ragtag.py --help

[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. ragtag.sh). For example:

set -e
module load ragtag
ragtag.py correct ref.fasta query.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] ragtag.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. ragtag.swarm). For example:

ragtag.py correct ref.fasta query1.fasta
ragtag.py correct ref.fasta query2.fasta
ragtag.py correct ref.fasta query3.fasta
ragtag.py correct ref.fasta query4.fasta

Submit this job using the swarm command.

swarm -f ragtag.swarm [-g #] [-t #] --module ragtag
-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 ragtag Loads the ragtag module for each subjob in the swarm