Biowulf High Performance Computing at the NIH
Transabyss on Biowulf

Transabyss perform de novo assembly of RNA-Seq data using ABySS. It comes with 2 main applications:

References:

If you use Trans-ABySS, please cite:

Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)

Documentation

https://github.com/bcgsc/transabyss/wiki

 

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@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 transabyss

[user@cn3144 ~]$ cd /data/$USER/dir

[user@cn3144 ~]$ transabyss-merge --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. transabyss.sh). For example:

#!/bin/bash
module load transabyss 
cd /data/$USER/dir 
transabyss-merge a.fa b.fa --threads $SLURM_CPUS_PER_TASK --mink 32 --maxk 64

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 transabyss.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. transabyss.swarm). For example:

cd /data/user/run1/; transabyss-merge a.fa b.fa --threads $SLURM_CPUS_PER_TASK --mink 32 --maxk 64 
cd /data/user/run2/; transabyss-merge a.fa b.fa --threads $SLURM_CPUS_PER_TASK --mink 32 --maxk 64 
cd /data/user/run3/; transabyss-merge a.fa b.fa --threads $SLURM_CPUS_PER_TASK --mink 32 --maxk 64 
........

Submit this job using the swarm command.

swarm -t 4 -f transabyss.swarm --module transabyss.swarm
where
--module transabyss Loads the transabyss module for each subjob in the swarm