Maker-Sapelo2 - Revision history

Shtsai at 18:34, 6 May 2026

2026-05-06T18:34:30Z

← Older revision		Revision as of 14:34, 6 May 2026
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	== Author / Distributor ==		== Author / Distributor ==

	[~~http~~://~~www~~.~~yandell~~-~~lab.org/software~~/~~index.html~~ Yandell-lab]		[https://github.com/Yandell-Lab/maker Yandell-lab]

	== Description ==		== Description ==
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	More details from http://gmod.org/wiki/MAKER_Tutorial#What_does_MAKER_do.3F		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 [http://gmod.org/wiki/GBrowse GBrowse], [http://gmod.org/wiki/JBrowse JBrowse], [http://gmod.org/wiki/Chado Chado], and [http://gmod.org/wiki/Apollo Apollo]~~.		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.

	== Running Program ==		== Running Program ==
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	== Installation ==		== Installation ==

	Source download from ~~http~~://~~www~~.~~yandell~~-~~lab.org~~/		Source download from https://github.com/Yandell-Lab/maker

	== System ==		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 01:03, 5 April 2026

2026-04-05T01:03:26Z

← Older revision		Revision as of 21:03, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	3.01.04		3.01.04

	=== Author / Distributor ===		== Author / Distributor ==

	[http://www.yandell-lab.org/software/index.html Yandell-lab]		[http://www.yandell-lab.org/software/index.html Yandell-lab]

	=== Description ===		== Description ==

	More details from http://gmod.org/wiki/MAKER_Tutorial#What_does_MAKER_do.3F		More details from http://gmod.org/wiki/MAKER_Tutorial#What_does_MAKER_do.3F
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	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 [http://gmod.org/wiki/GBrowse GBrowse], [http://gmod.org/wiki/JBrowse JBrowse], [http://gmod.org/wiki/Chado Chado], and [http://gmod.org/wiki/Apollo Apollo].		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 [http://gmod.org/wiki/GBrowse GBrowse], [http://gmod.org/wiki/JBrowse JBrowse], [http://gmod.org/wiki/Chado Chado], and [http://gmod.org/wiki/Apollo Apollo].

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	</pre>		</pre>

	==== Running maker in a MPI job ====		=== Running maker in a MPI job ===

	Here is an example of submission script (sub.sh) for running maker in a MPI job of 60 MPI processes running on 5 nodes:		Here is an example of submission script (sub.sh) for running maker in a MPI job of 60 MPI processes running on 5 nodes:
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	</pre>		</pre>

	==== Running maker in a memory-sharing threaded job ====		=== Running maker in a memory-sharing threaded job ===

	The maker command provides the -cpus option to specify how many threads to use for BLAST+.		The maker command provides the -cpus option to specify how many threads to use for BLAST+.
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	</pre>		</pre>

	==== Running maker in a single-core job ====		=== Running maker in a single-core job ===

	Here is an example of submission script (sub.sh) for running maker in a single-core job:		Here is an example of submission script (sub.sh) for running maker in a single-core job:
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	Maker wiki site is at https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page		Maker wiki site is at https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]
	=== Installation ===		== Installation ==

	Source download from http://www.yandell-lab.org/		Source download from http://www.yandell-lab.org/

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 19:28, 28 March 2025

2025-03-28T19:28:46Z

← Older revision		Revision as of 15:28, 28 March 2025
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	Then submit the job by:		Then submit the job by:
	<pre class="gcommand">		<pre class="gcommand">
	~~qsub~~ ./sub.sh		sbatch ./sub.sh
	</pre>		</pre>

Shtsai: /* Running maker in a memory-sharing threaded job */

2025-03-25T21:27:57Z

Running maker in a memory-sharing threaded job

← Older revision		Revision as of 17:27, 25 March 2025
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	==== Running maker in a memory-sharing threaded job ====		==== Running maker in a memory-sharing threaded job ====

			The maker command provides the -cpus option to specify how many threads to use for BLAST+.

	Here is an example of submission script (sub.sh) for running maker in a threaded job of 16 threads running on 1 node:		Here is an example of submission script (sub.sh) for running maker in a threaded job of 16 threads running on 1 node:
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	maker -cpus 16		maker -cpus 16
	</pre>		</pre>

	==== Running maker in a single-core job ====		==== Running maker in a single-core job ====

Shtsai: /* Running maker in a MPI job */

2025-03-25T21:26:55Z

Running maker in a MPI job

← Older revision		Revision as of 17:26, 25 March 2025
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	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --job-name=maker-mpi		#SBATCH --job-name=maker-mpi
			#SBATCH --nodes=1
	#SBATCH --ntasks=16		#SBATCH --ntasks=16
	#SBATCH --cpus-per-task=1		#SBATCH --cpus-per-task=1
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	srun $EBROOTMAKER/bin/maker		srun $EBROOTMAKER/bin/maker
	</pre>		</pre>

	==== Running maker in a memory-sharing threaded job ====		==== Running maker in a memory-sharing threaded job ====

Shtsai at 21:26, 25 March 2025

2025-03-25T21:26:34Z

← Older revision		Revision as of 17:26, 25 March 2025
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	Command "maker -CTL" will generate the configuration files '''maker_bopts.ctl''', '''maker_evm.ctl''', '''maker_exe.ctl''', and '''maker_opts.ctl''' in your working folder. You need to configure those configuration files before you run maker. Examples can be found at [http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Running_MAKER_with_example_data Running_MAKER_with_example_data].		Command "maker -CTL" will generate the configuration files '''maker_bopts.ctl''', '''maker_evm.ctl''', '''maker_exe.ctl''', and '''maker_opts.ctl''' in your working folder. You need to configure those configuration files before you run maker. Examples can be found at [http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#Running_MAKER_with_example_data Running_MAKER_with_example_data].

			To use an MPI-enabled version:
			<pre class="gscript">
			module load MAKER/3.01.04-foss-2022a-MPI
			</pre>

	==== Running maker in a MPI job ====		==== Running maker in a MPI job ====
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml MAKER/3.01.04-foss-2022a		ml MAKER/3.01.04-foss-2022a-MPI

	srun $EBROOTMAKER/bin/maker		srun $EBROOTMAKER/bin/maker

Shtsai at 17:48, 21 March 2025

2025-03-21T17:48:28Z

← Older revision		Revision as of 13:48, 21 March 2025
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	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --job-name=maker-mpi		#SBATCH --job-name=maker-mpi
	#SBATCH --ntasks=60		#SBATCH --ntasks=16
	~~#SBATCH --ntasks-per-node=12~~
	#SBATCH --cpus-per-task=1		#SBATCH --cpus-per-task=1
	#SBATCH --mem-per-cpu=1G		#SBATCH --mem-per-cpu=1G
	#SBATCH --time=8:00:00		#SBATCH --time=24:00:00
	#SBATCH --output=log.o%j		#SBATCH --output=log.o%j
	#SBATCH --export=NONE		#SBATCH --export=NONE
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	ml MAKER/3.01.04-foss-2022a		ml MAKER/3.01.04-foss-2022a

	~~mpirun -n 60~~ maker		srun $EBROOTMAKER/bin/maker
	</pre>		</pre>

Shtsai at 19:25, 31 January 2025

2025-01-31T19:25:17Z

← Older revision		Revision as of 15:25, 31 January 2025
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	ml MAKER/3.01.04-foss-2022a		ml MAKER/3.01.04-foss-2022a

	maker -~~cpu~~ 16		maker -cpus 16
	</pre>		</pre>

Chelsea: /* Version 3.01.04 */

2023-09-06T15:06:19Z

Version 3.01.04

← Older revision		Revision as of 11:06, 6 September 2023
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	=== Version ===		=== Version ===

	3.01.03		3.01.04

	=== Author / Distributor ===		=== Author / Distributor ===
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	Version 3.01.03 is installed at /apps/gb/Maker/3.01.03		Version 3.01.04 is installed at /apps/eb/Maker/3.01.04-foss-2022a

	Example to prepare the configuration files.		Example to prepare the configuration files.
	<pre class="gscript">		<pre class="gscript">
	module load ~~Maker~~/3.01.03		module load MAKER/3.01.04-foss-2022a
	maker -CTL		maker -CTL
	</pre>		</pre>
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml ~~Maker~~/3.01.03		ml MAKER/3.01.04-foss-2022a

	mpirun -n 60 maker		mpirun -n 60 maker
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml ~~Maker~~/3.01.03		ml MAKER/3.01.04-foss-2022a

	maker -cpu 16		maker -cpu 16
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml ~~Maker~~/3.01.03		ml MAKER/3.01.04-foss-2022a

	maker		maker
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	<pre class="gcommand">		<pre class="gcommand">
	ml ~~Maker~~/3.01.03		ml MAKER/3.01.04-foss-2022a
	maker -h		maker -h

	MAKER version 3.01.03		MAKER version 3.01.04

	Usage:		Usage:
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	-help\|? Prints this usage statement.		-help\|? Prints this usage statement.

	</pre>		</pre>

Moses at 14:54, 2 November 2020

2020-11-02T14:54:18Z

← Older revision		Revision as of 10:54, 2 November 2020
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	=== Running Program ===		=== Running Program ===

	Also refer to [[Running Jobs on ~~Sap2test~~]]		Also refer to [[Running Jobs on Sapelo2]]

	Version 3.01.03 is installed at /apps/gb/Maker/3.01.03		Version 3.01.03 is installed at /apps/gb/Maker/3.01.03