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BWA
Overview
BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. There are three algorithms implemented – BWA-backtrack, BWA-SW and BWA-MEM – see the BWA website for advice on which to use.
Versions 0.7.15, 0.7.5a and 0.7.17 are installed on the CSF. They were compiled with gcc 4.7.0.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license and all usage must adhere to that license.
Please cite your usage of this software as detailed on the BWA website.
Set up procedure
To access the software you must first load one of the following the modulefiles:
module load apps/gcc/bwa/0.7.17 module load apps/gcc/bwa/0.7.15 module load apps/gcc/bwa/0.7.5a
Running the application
Please do not run BWA on the login node. Jobs should be submitted to the compute nodes via batch.
A full description of all of the BWA commands and flags accepted by the application is beyond the scope of this web-page.
However, you may run the following command on the login node to see a list of flag / args that the application will accept. These should be used in your jobscript:
man bwa (press 'space' to page down through the help text, q to quit)
You may also run the following command on the login node to see a summary of commands and flags accepted by the application:
bwa
To see the help text for a specific bwa command, run:
bwa command
For example:
bwa fastmap
You must check whether the command you are using accepts a flag to specify the number of threads (cores) to use. This should then be applied to the command-line in your jobscript.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # These commands will only use one core bwa index args... bwa samse args... bwa sampe args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Number of cores to use (can be 2 -- 24) # $NSLOTS is automatically set to the number of cores specified above # These commands can be run using multiple cores bwa mem -t $NSLOTS args... bwa aln -t $NSLOTS args... bwa bwasw -t $NSLOTS args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.