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Use the module name maker to discover versions available and to load the application.
From what we have observed and learnt from existing users, maker is typically used along side augustus and exonerate.
Beartooth Module Setup:
As part of the installation of On Beartooth, version 3.01.04 on Beartooth, when you module load make/3.01.04 it will automatically load the following automatically loads the following additional modules:
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snap-korf/20212022-11-0406 repeatmasker/4.1.3-ompi exonerate/2.4.0 perl-bioperl/1.7.6 blast-plus/2.13.0 |
Teton Modules
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module load gcc/7.3.0 maker/2.31.10 augustus/3.3.2-py27 exonerate/2.4.0-py27 |
Please use the module spider command to look for alternatives.
Control Files
When setting up a new maker environment, a user will typically run make -CTL to generate the core three control files:
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Running maker -CTL will generate a file with the following paths:
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If you require augustus then load it as a module.
Teton Example:
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maker_opts.ctl
On Beartooth
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running repeat masker. #--------- command -------------# Widget::RepeatMasker: cd /tmp/maker_4xxbhq; /apps/u/spack/gcc/12.2.0/repeatmasker/4.1.2-p1-vwpy6c4/bin/RepeatMasker /pfs/tc1/project/arcc/software/maker/testing/maker_tutorial/example_01_basic/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/project/arcc/software/maker/testing/maker_tutorial/example_01_basic/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1 #-------------------------------# Species "all" is not known to RepeatMasker. There may not be any TE families defined in the libraries for this species/clade or there may be an error in the spelling. Please check your entry against the NCBI Taxonomy database and/or try using a broader clade or related species instead. The full list of species/clades defined in the library may be obtained using the famdb.py script. |
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cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI) |
Teton Script Templates
What follows are two example scripts, one for a single node/single cpu, and another for multiple nodes using multiple tasks.
Single Node
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Multicore
Maker can be used across multiple nodes, by setting, for example:
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#!/bin/bash #SBATCH --nodes=14 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=1 ... module load gcc/7.3.0 maker/2.31.10 augustus/3.3.2-py27 exonerate/2.4.0-py27 maker |
Multiple Nodes
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8 |
On Teton run the following:
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#!/bin/bash
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1
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# Modules to Load
module load gcc/7.3.0 maker/2.31.10 augustus/3.3.2-py27 exonerate/2.4.0-py27
mpiexec -n 32 maker |
Notice that the line to start maker has changed, with With the value after the -n option equaling the number of nodes multiplied by the number of tasks (4 x 8 = 32).
On Beartooth, simply run:
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srun maker |
Memory Issues
Memory is always an issue with any form of bioinformatics analysis, and there are no straight forward recommendations we can make. As a researcher you’ll need to track the size of your data sets, the type of analysis, and the resources you’ve requested and how efficiently they’ve been used.
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