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SOAP on Biowulf

SOAP has been in evolution from a single alignment tool to a tool package that provides full solution to next generation sequencing data analysis. Currently, it consists of several programs:

SOAP3
SOAP2
SOAPsnp
SOAPsv
SOAPfuse
SOAP-PopIndel
SOAPindel
SOAPHla
SOAPsplice
SOAPdenovo
SOAPals
SOAPfusion
SOAPsnp 

A GPU-accelerated alignment tool called SOAP3 is also available on Biowulf. (SOAP3 on Biowulf)

Program Location

All the SOAP packages are installed in /usr/local/apps/soap/. The command 'module load soap' will add the latest version of each package executables to your path. Versions of each package can be seen with the 'module show soap' command.

Submitting a single batch job

1. Create a script file. The file will contain the lines similar to the lines below.

#!/bin/bash
# This file is soapScript
#
#PBS -N soap
#PBS -m be
#PBS -k oe

module load soap

cd /data/user/soap/run1

# align single-end reads with soap, using 16 threads
soap -a reads_a -D index_files -o output -n 16

# align paired-end reads and detect splice junctions with soapsplice, 16 threads
soapsplice -d 2BWT_INDEX_PREFIX -l reads_a -r length_of_reads -I insert_length -o output_prefix -p 16

# diploid genome resequencing
soapsnp -i  -d  -o  -r 0.00005 -e 0.0001 -t -u -L  -M 

Note:

2. Submit the script using the 'qsub' command on Biowulf.

$ qsub -l nodes=1:x2800 ./script

Note: here 'x2800' was specified which means the job will be running on one 'x2800' node. Depending on the number of threads specified and the amount of memory required, different types of nodes can be specified instead of x2800. Run 'freen' to check for current availabe node types and numbers.

Running an interactive job

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

First set the paths using 'module load soap'. Allocate an interactive node as described below, and run the interactive job there.

biowulf% qsub -I -l nodes=1:g24:c16
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready
      
[user@p2013]$ module load soap

[user@p2013]$ cd /data/user/myruns

[user@p2013]$ soap -a reads_a -D index_files -o output -n 16
 
[user@p2013]$ soapsplice -d 2BWT_INDEX_PREFIX -l reads_a -r length_of_reads -I insert_length -o output_prefix -p 16

[user@p2013]$ exit
qsub: job 2236960.biobos completed
[user@biowulf ~]$

Documentation

http://soap.genomics.org.cn/