MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=20g -n 4
[user@cn4337 ~]$ module load maker/3.01.04
[+] Loading augustus 3.4.0 on cn0826
[+] Loading singularity 4.1.5 on cn0826
[+] Loading bedtools 2.30.0
[+] Loading blast 2.15.0+ ...
[+] Loading BLAT 3.5
[+] Loading busco 5.4.7
Busco Config File /home/denisovga/busco.config exists
Augustus Config Directory /home/denisovga/augustus.config exists
[+] Loading exonerate, version 2.4.0...
[+] Loading gcc 9.2.0 ...
[+] Loading openmpi/5.0.5/ucx-1.17.0 gcc-9.2.0 ...
[+] Loading perl 5.36 on cn0826
[+] Loading python 3.8 ...
[+] Loading repeatmasker 4.1.7-p1 on cn0826
[+] Loading repeatmodeler 2.0.1 on cn0826
[+] Loading trf, version 4.09.1...
[+] Loading ucsc 445 on cn0826
[+] Loading maker 3.01.04
[user@cn4337 ~]$ maker -h
MAKER version 3.01.04
Usage:
maker [options]
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 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 Set the base name MAKER uses to save output files.
MAKER uses the input genome file name by default.
-tries|t Run contigs up to the specified number of tries.
-cpus|c 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
In order to use maker, copy sample data to your current folder:
[user@cn4337 ~]$ cp $MAKER_DATA/*fasta .Create control file templates:
[user@cn4337 ~]$ maker -CTL [user@cn4337 ~]$ ls *ctl maker_bopts.ctl maker_evm.ctl maker_exe.ctl maker_opts.ctlEdit these files properly, by adding a missing information to each line before the symbol '#'.
[user@cn4337 ~]$ cp $MAKER_HOME/*ctl .Now you can run maker by passing it the edited control files as input:
[user@cn4337 ~]$ mpiexec -n 4 maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... STATUS: Setting up database for any GFF3 input... A data structure will be created for you at: /gpfs/gsfs7/users/user/MAKER/genome.maker.output/genome_datastore To access files for individual sequences use the datastore index: /gpfs/gsfs7/users/user/MAKER/genome.maker.output/genome_master_datastore_index.log STATUS: Now running MAKER... examining contents of the fasta file and run log ... --Next Contig-- Processing run.log file... MAKER WARNING: The file genome.maker.output/genome_datastore/46/63/chr13//theVoid.chr13/0/chr13.7.te_proteins%2Efa sta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now starting the contig!! SeqID: chr13 Length: 114364328 #--------------------------------------------------------------------- examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file genome.maker.output/genome_datastore/63/A4/chr14//theVoid.chr14/0/chr14.0.te_proteins%2Efa sta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now starting the contig!! SeqID: chr14 Length: 107043718 #--------------------------------------------------------------------- examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file genome.maker.output/genome_datastore/F7/6D/chr15//theVoid.chr15/0/chr15.1.te_proteins%2Efa sta.repeatrunner did not finish on the last run and must be erased #--------------------------------------------------------------------- Now starting the contig!! SeqID: chr15 Length: 101991189 #--------------------------------------------------------------------- examining contents of the fasta file and run log ... --Next Contig-- Processing run.log file... Maker is now finished!!!End the interactive session:
[user@cn4337 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$