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RAPSearch (protein similarity search)

Table of Contents

Introduction

RAPSearch (Reduced Alphabet-based Protein similarity Search) and its successor RAPSearch2 are programs for the analysis of next-generation sequencing data (short reads). 

Caution: Documentation for the program is very sparse, so, it is not clear whether it would be preferable to use multiple threads with RAPSearch2 or use the Python wrapper with RAPSearch that splits the calculation into pieces that can be run on separate processors.  Only RAPSearch2 was installed, to allow a researcher to explore its use.

Running RAPSearch2 on Breezy

RAPSearch2, version 2.23, was installed on Breezy.  The rapsearch and prerapsearch binaries are in /global/software/rapsearch/rapsearch223/bin.  To obtain a list of command line arguments type:

/global/software/rapsearch/rapsearch223/bin/rapsearch - -h

The -z argument is used to specify the number of threads to use.  This should be set to $PBS_NUM_PPN in your batch job script so that the number of threads matches the number of cores requested of the batch job system.  For example, if you request 4 cores with -l nodes=1:ppn=4, your job script would look like:

#PBS -l nodes=1:ppn=4
#PBS -l mem=8gb
...
/global/software/rapsearch/rapsearch223/bin/rapsearch -z $PBS_NUM_PPN ... (other command line arguments)

2015-04-21 - Page created.

System Jasper Breezy
Version 2.23 2.23