Maker-Sapelo2
Category
Bioinformatics
Program On
Sap2test
Version
3.01.03
Author / Distributor
Description
More details from http://gmod.org/wiki/MAKER_Tutorial#What_does_MAKER_do.3F
MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience; however, MAKER is also designed to be scalable and is appropriate for projects of any size even including use by large sequence centers. MAKER can be used for de novo annotation of newly sequenced genomes, for updating existing annotations to reflect new evidence, or just to combine annotations, evidence, and quality control statistics for use in other GMOD programs like GBrowse, JBrowse, Chado, and Apollo.
Running Program
Also refer to Running Jobs on Sapelo2
Version 3.01.03 is installed at /apps/gb/Maker/3.01.03
Example to prepare the configuration files.
module load Maker/3.01.03
maker -CTL
Command "maker -CTL" will generate the configuration files maker_bopts.ctl, maker_evm.ctl, maker_exe.ctl, maker_opts.ctl.
Here is the example of submission script for running make in a MPI job of 60 MPI processes on 5 nodes:
#!/bin/bash #SBATCH --partition=batch #SBATCH --job-name=Maker #SBATCH --ntasks=60 #SBATCH --ntasks-per-node=12 #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=2G #SBATCH --time=24:00:00 #SBATCH --output=log.o%j #SBATCH --export=NONE export OMPI_MCA_mpi_warn_on_fork=0 unset SLURM_EXPORT_ENV cd $SLURM_SUBMIT_DIR ml Maker/3.01.03 mpirun -n 60 maker
Then submit the job by:
qsub ./sub.sh
Version 2.31.9_conda is installed at /usr/local/apps/gb/maker/2.31.9_conda via Conda. The sample data and sample control files are at /usr/local/apps/gb/maker/2.31.9_conda/data
Example of the conda version script sub.sh to run on at queue. First step is to prepare the configuration files. Here uses /scratch/yhuang/08202018a as an example of working dir:
ml Miniconda3/4.4.10
. /usr/local/apps/eb/Miniconda3/4.4.10/etc/profile.d/conda.sh
conda activate /usr/local/apps/gb/maker/2.31.9_conda
cd /scratch/yhuang/08202018a
maker -CTL
cp /usr/local/apps/gb/maker/2.31.9_conda/data/maker_exe.ctl /usr/local/apps/gb/maker/2.31.9_conda/data/maker_opts.ctl .
Command "maker -CTL" will generate the configuration files. At the central location, the maker_exe.ctl and maker_opts.ctl are further configured for more application dependencies. So here copies from the central files.
Here is the example of submission script:
#PBS -S /bin/bash
#PBS -N j_maker
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=8:00:00
#PBS -l mem=10gb
#PBS -M username@uga.edu
#PBS -m abe
ml Miniconda3/4.4.10
. /usr/local/apps/eb/Miniconda3/4.4.10/etc/profile.d/conda.sh
conda activate /usr/local/apps/gb/maker/2.31.9_conda
mkdir -p /tmp/lscratch/$PBS_JOBID/tmp
maker [options] -TMP /tmp/lscratch/$PBS_JOBID/tmp <maker_opts> <maker_bopts> <maker_exe>
conda deactivate
Then submit the job by:
qsub ./sub.sh
Version 2.31.10 is installed in /usr/local/apps/gb/Maker/2.31.10
To use this version of Maker, please first load the module with
module load Maker/2.31.10-foss-2016b
This module will automatically load its dependencies. This version was compiled with MPI support and loading this module will also load the appropriate OpenMPI modules and set LD_PRELOAD to point to the correct MPI library.
Documentation
Version 3.01.02-beta
MAKER version 3.01.02
Usage:
maker [options] <maker_opts> <maker_bopts> <maker_exe>
Description:
MAKER is a program that produces gene annotations in GFF3 format using
evidence such as EST alignments and protein homology. MAKER can be used to
produce gene annotations for new genomes as well as update annotations
from existing genome databases.
The three input arguments are control files that specify how MAKER should
behave. All options for MAKER should be set in the control files, but a
few can also be set on the command line. Command line options provide a
convenient machanism to override commonly altered control file values.
MAKER will automatically search for the control files in the current
working directory if they are not specified on the command line.
Input files listed in the control options files must be in fasta format
unless otherwise specified. Please see MAKER documentation to learn more
about control file configuration. MAKER will automatically try and
locate the user control files in the current working directory if these
arguments are not supplied when initializing MAKER.
It is important to note that MAKER does not try and recalculated data that
it has already calculated. For example, if you run an analysis twice on
the same dataset you will notice that MAKER does not rerun any of the
BLAST analyses, but instead uses the blast analyses stored from the
previous run. To force MAKER to rerun all analyses, use the -f flag.
MAKER also supports parallelization via MPI on computer clusters. Just
launch MAKER via mpiexec (i.e. mpiexec -n 40 maker). MPI support must be
configured during the MAKER installation process for this to work though
Options:
-genome|g <file> Overrides the genome file path in the control files
-RM_off|R Turns all repeat masking options off.
-datastore/ Forcably turn on/off MAKER's two deep directory
nodatastore structure for output. Always on by default.
-old_struct Use the old directory styles (MAKER 2.26 and lower)
-base <string> Set the base name MAKER uses to save output files.
MAKER uses the input genome file name by default.
-tries|t <integer> Run contigs up to the specified number of tries.
-cpus|c <integer> Tells how many cpus to use for BLAST analysis.
Note: this is for BLAST and not for MPI!
-force|f Forces MAKER to delete old files before running again.
This will require all blast analyses to be rerun.
-again|a recaculate all annotations and output files even if no
settings have changed. Does not delete old analyses.
-quiet|q Regular quiet. Only a handlful of status messages.
-qq Even more quiet. There are no status messages.
-dsindex Quickly generate datastore index file. Note that this
will not check if run settings have changed on contigs
-nolock Turn off file locks. May be usful on some file systems,
but can cause race conditions if running in parallel.
-TMP Specify temporary directory to use.
-CTL Generate empty control files in the current directory.
-OPTS Generates just the maker_opts.ctl file.
-BOPTS Generates just the maker_bopts.ctl file.
-EXE Generates just the maker_exe.ctl file.
-MWAS <option> Easy way to control mwas_server for web-based GUI
options: STOP
START
RESTART
-version Prints the MAKER version.
-help|? Prints this usage statement.
Version 2.31.9_cond
ml Miniconda3/4.4.10
conda activate /usr/local/apps/gb/maker/2.31.9_conda
maker -h
MAKER version 2.31.9
Usage:
maker [options] <maker_opts> <maker_bopts> <maker_exe>
Description:
MAKER is a program that produces gene annotations in GFF3 format using
evidence such as EST alignments and protein homology. MAKER can be used to
produce gene annotations for new genomes as well as update annotations
from existing genome databases.
The three input arguments are control files that specify how MAKER should
behave. All options for MAKER should be set in the control files, but a
few can also be set on the command line. Command line options provide a
convenient machanism to override commonly altered control file values.
MAKER will automatically search for the control files in the current
working directory if they are not specified on the command line.
Input files listed in the control options files must be in fasta format
unless otherwise specified. Please see MAKER documentation to learn more
about control file configuration. MAKER will automatically try and
locate the user control files in the current working directory if these
arguments are not supplied when initializing MAKER.
It is important to note that MAKER does not try and recalculated data that
it has already calculated. For example, if you run an analysis twice on
the same dataset you will notice that MAKER does not rerun any of the
BLAST analyses, but instead uses the blast analyses stored from the
previous run. To force MAKER to rerun all analyses, use the -f flag.
MAKER also supports parallelization via MPI on computer clusters. Just
launch MAKER via mpiexec (i.e. mpiexec -n 40 maker). MPI support must be
configured during the MAKER installation process for this to work though
Options:
-genome|g <file> Overrides the genome file path in the control files
-RM_off|R Turns all repeat masking options off.
-datastore/ Forcably turn on/off MAKER's two deep directory
nodatastore structure for output. Always on by default.
-old_struct Use the old directory styles (MAKER 2.26 and lower)
-base <string> Set the base name MAKER uses to save output files.
MAKER uses the input genome file name by default.
-tries|t <integer> Run contigs up to the specified number of tries.
-cpus|c <integer> Tells how many cpus to use for BLAST analysis.
Note: this is for BLAST and not for MPI!
-force|f Forces MAKER to delete old files before running again.
This will require all blast analyses to be rerun.
-again|a recaculate all annotations and output files even if no
settings have changed. Does not delete old analyses.
-quiet|q Regular quiet. Only a handlful of status messages.
-qq Even more quiet. There are no status messages.
-dsindex Quickly generate datastore index file. Note that this
will not check if run settings have changed on contigs
-nolock Turn off file locks. May be usful on some file systems,
but can cause race conditions if running in parallel.
-TMP Specify temporary directory to use.
-CTL Generate empty control files in the current directory.
-OPTS Generates just the maker_opts.ctl file.
-BOPTS Generates just the maker_bopts.ctl file.
-EXE Generates just the maker_exe.ctl file.
-MWAS <option> Easy way to control mwas_server for web-based GUI
options: STOP
START
RESTART
-version Prints the MAKER version.
-help|? Prints this usage statement.
Installation
Conda
System
64-bit Linux