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Gubbins
Overview
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
Version 2.3.2 is installed on the CSF. This can use Anaconda Python v5.1.0 (python 3.6.4).
Restrictions on use
There are no restrictions on accessing Gubbins on the CSF. The source is released under the GNU GPL v2 license.
Set up procedure
To access the software you must first load one of the following modulefile:
module load apps/gcc/python-packages/anaconda3-5.1.0/gubbins/2.3.2
The modulefile will automatically load the required version of Anaconda modulefile for you.
Running the application
Please do not run Gubbins on the login node. Jobs should be submitted to the compute nodes via batch.
Ensure that your python script reads the number of cores your job has reserved in the batch system by getting the $NSLOTS environment variable. You should then pass this value to the Gubbins python functions to ensure your code only uses that number of cores.
run_gubbins.py [FASTA alignment]
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings run_gubbins.py [FASTA alignment]
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 #$ -S /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 (2-24) # You must ensure your python script reads the $NSLOTS environment variable # to obtain the correct number of cores to use. run_gubbins.py [FASTA alignment] --threads $NSLOTS
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.