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EMIRGE
Overview
EMIRGE is a program to reconstruct full length ribosomal genes from short read sequencing data. In the process, it also provides estimates of the sequences’ abundances.
Version 0.61.1 is installed on the CSF. This will use python 2.7 provided by Anaconda Python 2.5.0.
EMIRGE will use the usearch application installed on the CSF. Please follow the link to the CSF usearch page to see how to obtain access to this restricted application.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the GPL v3 license and all usage should fall within that license.
Please cite your usage of this software in your research by citing the references listed in the EMIRGE github page.
Set up procedure
To access the software you must first load one of the usearch modulefiles and then the emirge modulefile:
# If using emirge.py or emirge_amplicon.py load one of the usearch modulefiles first: module load apps/binapps/usearch/6.1.544 module load apps/binapps/usearch/8.0.1623 # If using emirge_makedb.py load the vsearch and bowtie modulefiles first: module load apps/binapps/vsearch/1.1.3 module load apps/binapps/bowtie/0.12.9 # Then load the emirge modulefile module load apps/gcc/python-packages/anaconda-2.5.0/emirge/0.61.1
You may run the following command on the login node to check the flags/switches that the application requires:
emirge.py --help
The following executables are available (which all accept the --help flag):
emirge_amplicon.py emirge_makedb.py emirge.py emirge_rename_fasta.py
You must run the application via a batch script when processing data.
Running the application
Please do not run emirge on the login node. Jobs should be submitted to the compute nodes via batch.
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 # $NSLOTS will be set to 1 (for 1 core) in a serial job emirge.py -a $NSLOTS args... emirge_amplicon.py -a $NSLOTS args... emirge_makedb.py -p $NSLOTS args... # Note -p flag (not -a) emirge_rename_fasta.py args... # This is a serial app
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -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 (2-24 permitted) # $NSLOTS will be set to the number of cores given on the -pe line above: emirge.py -a $NSLOTS args... emirge_amplicon.py -a $NSLOTS args... emirge_makedb.py -p $NSLOTS args... # Note -p flag (not -a) emirge_rename_fasta.py args... # This is a serial app
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.