Maker-Sapelo2: Difference between revisions

Revision as of 15:32, 8 September 2020

Program On

Sap2test

Version

3.01.03

Author / Distributor

Yandell-lab

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.

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Installation

Conda

System

64-bit Linux

Maker-Sapelo2: Difference between revisions

Revision as of 15:32, 8 September 2020

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Maker-Sapelo2: Difference between revisions

Revision as of 15:32, 8 September 2020

Category

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