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MaxBin
Overview
MaxBin2 is a program for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
Version 2.2.5 is installed on the CSF. Please note that the application incorrectly reports itself as version 2.2.4. This may be corrected in a future release but this is definitely version 2.2.5.
It was compiled with the GCC 4.9.0 compiler.
The auxiliary applications provided by MaxBin (IDBA-UD, HMMER3, Bowtie2, FragGeneScan) have been installed. While some of these already exists on the CSF (available via other modulefiles) the versions used by MaxBin are installed within the MaxBin installation and no further modulefiles are required.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the ?BSD license and any use should fall within the restrictions of that license. Please see the $MAXBINDIR/License text file on the CSF.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/maxbin/2.2.5
Running the application
Please do not run MaxBin on the login node. Jobs should be submitted to the compute nodes via batch.
You may run the command without any args on the login node to display the help text:
run_MaxBin.pl
Usage:
run_MaxBin.pl
-contig (contig file)
-out (output file)
...
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # $NSLOTS is automatically set to 1 in a serial job run_MaxBin.pl -thread $NSLOTS -contig contig_gile -out output_file other args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Number of cores (2-24 permitted) # $NSLOTS is automatically set to the number of cores requested above run_MaxBin.pl -thread $NSLOTS -contig contig_gile -out output_file other args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.