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AByss/Trans-AByss on Biowulf

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The parallel version is implemented using MPI and is capable of assembling larger genomes.

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

$ module avail abyss
-------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles --------------------------------------------------------
abyss/1.3.1 abyss/1.3.2 abyss/1.3.4 abyss/1.3.5(default) $ module load abyss $ module list Currently Loaded Modulefiles: 1) abyss/1.3.5
$ module unload abyss $ module load abyss/1.3.2 $ module show abyss ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/abyss/1.3.5: module-whatis Sets up abyss 1.3.5 prepend-path PATH /usr/local/apps/abyss/1.3.5/bin prepend-path PATH /usr/local/transabyss/bin prepend-path PATH /usr/local/OpenMPI/1.6/gnu/eth/bin -------------------------------------------------------------------
Submitting a single batch job

1. Create a script file. Sample batch script file

#!/bin/bash
# This file is abyssScript
#
#PBS -N abyss
#PBS -m be
#PBS -k oe

module load abyss
cd /data/user/mydir 

`which abyss-pe` np=48 k=25 n=10 in='InputFile1 InputFile2' name=OutfileNameHere

module load transabyss
python trans-abyss.py -<stage> -n <input file>

2. Submit the script using the 'qsub' command on Biowulf, with, for example:

$ qsub -l nodes=3:g24:c16 ./script

This job will run on 3x g24 (24 GB of memory) nodes. Note, the 'np' in the script is set to be 48 because the job is submitted to 3 g24:c16 nodes. So the total cores available are 16x3=48. If the job is submitted to 2x g8 nodes which has 4 cores each, then np=8 should be used in the script.

Running an interactive job

Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node.

biowulf% qsub -I -l nodes=1:g24:c16
qsub: waiting for job 2236960.biobos to start
      qsub: job 2236960.biobos ready

[user@pxxx]$ module load abyss      
[user@pxxx]$ cd /data/user/myruns
[user@pxxx]$ `which abyss-pe` np=16 k=25 n=10 in='input1.fastq input2.fastq' name=dog
[user@pxxx]$ module load transabyss 
[user@pxxx]$ python trans-abyss.py -<stage> -n <input file>
[user@p70]$ exit
qsub: job 2236960.biobos completed

[user@biowulf ~]$ 



Documentation

http://www.bcgsc.ca/platform/bioinfo/software/abyss

http://www.bcgsc.ca/downloads/trans-abyss/data/trans-abyss-manual-v1.4.4.pdf