BUSCO-Sapelo2 - Revision history

Shtsai at 00:18, 5 April 2026

2026-04-05T00:18:59Z

← Older revision		Revision as of 20:18, 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 ==
	<!--		<!--
	2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2		2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2
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	5.8.3		5.8.3

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

	[https://busco.ezlab.org/ BUSCO]		[https://busco.ezlab.org/ BUSCO]

	=== Description ===		== Description ==
	"BUSCO - Benchmarking sets of Universal Single-Copy Orthologs."		"BUSCO - Benchmarking sets of Universal Single-Copy Orthologs."
	More details are at [https://busco.ezlab.org/ BUSCO]		More details are at [https://busco.ezlab.org/ BUSCO]

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

	<!--		<!--
	==== Version 5.4.7 ====		=== Version 5.4.7 ===

	* Version 5.4.7, is installed at /apps/eb/BUSCO/5.4.7-foss-2022a		* Version 5.4.7, is installed at /apps/eb/BUSCO/5.4.7-foss-2022a
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	</pre>		</pre>

	==== Version 5.5.0 ====		=== Version 5.5.0 ===

	* Version 5.5.0, is installed at /apps/eb/BUSCO/5.5.0-foss-2022a		* Version 5.5.0, is installed at /apps/eb/BUSCO/5.5.0-foss-2022a
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	where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.		where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.

	==== Version 5.8.2, Singularity Image ====		=== Version 5.8.2, Singularity Image ===

	* Version 5.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif		* Version 5.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif
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	</pre>		</pre>

	===~~= ersion~~ 4.0.5, Singularity Image ====		=== Version 4.0.5, Singularity Image ===

	* version 2.0 is installed as a singularity image at /apps/singularity-images/busco-2.0.simg		* version 2.0 is installed as a singularity image at /apps/singularity-images/busco-2.0.simg

	==== Version 4.0.5, Singularity Image ====		=== Version 4.0.5, Singularity Image ===

	* Version 4.0.5, is installed as a singularity image at /apps/singularity-images/busco-4.0.5.simg		* Version 4.0.5, is installed as a singularity image at /apps/singularity-images/busco-4.0.5.simg
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	==== Version 5.8.3 ====		=== Version 5.8.3 ===

	* Version 5.8.3, is installed at /apps/eb/BUSCO/5.8.3-foss-2023a		* Version 5.8.3, is installed at /apps/eb/BUSCO/5.8.3-foss-2023a
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	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is obtained from [https://gitlab.com/ezlab/busco/ BUSCO]		Source code is obtained from [https://gitlab.com/ezlab/busco/ BUSCO]

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

Chelsea at 14:50, 8 July 2025

2025-07-08T14:50:18Z

← Older revision		Revision as of 10:50, 8 July 2025
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	2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2		2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2
	-->		-->
	5.8.2		5.8.3

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

Chelsea at 14:50, 8 July 2025

2025-07-08T14:50:06Z

← Older revision		Revision as of 10:50, 8 July 2025
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	=== Version ===		=== Version ===
			<!--
	2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2		2.0, 4.0.5, 5.4.7, 5.5.0, 5.8.2
			-->
			5.8.2

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

			<!--
	==== Version 5.4.7 ====		==== Version 5.4.7 ====

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	sbatch sub.sh		sbatch sub.sh
	</pre>		</pre>
			-->




			==== Version 5.8.3 ====

			* Version 5.8.3, is installed at /apps/eb/BUSCO/5.8.3-foss-2023a

			To use this version of BUSCO, please first load the module with
			<pre class="gcommand">
			ml BUSCO/5.8.3-foss-2023a
			</pre>

			BLAST+ v2.14.1 is loaded with this application. This version of Blast+ enables the multiple cores function for busco. AUGUSTUS v3.5.0 is also loaded with AUGUSTUS_CONFIG_PATH set correctly.

			Before run the program, please copy the BUSCO config file config.ini to your current working folder and modify the input file value and other values as needed in it. Please also copy AUGUSTUS config folder to the place:

			<pre class="gscript">
			cp -r /apps/eb/AUGUSTUS/3.5.0-foss-2023a/config config_augustus
			export AUGUSTUS_CONFIG_PATH=config_augustus

			cp /apps/eb/BUSCO/5.8.3-foss-2023a/config/config.ini config.ini
			vim config.ini
			export BUSCO_CONFIG_FILE=config.ini
			</pre>

			'''Example shell script''' sub.sh to run BUSCO/5.8.3 on the batch partition:
			<pre class="gscript">
			#!/bin/bash
			#SBATCH --job-name=busco # Job name
			#SBATCH --partition=batch # Partition (queue) name
			#SBATCH --ntasks=1 # Run a single task
			#SBATCH --cpus-per-task=4 # Number of CPU cores per task
			#SBATCH --mem=10gb # Job memory request
			#SBATCH --time=48:00:00 # Time limit hrs:min:sec
			#SBATCH --output=log.%j.out # Standard output log
			#SBATCH --error=log.%j.err # Standard error log
			#SBATCH --export=NONE # Don't export user's explicit env variables to compute node
			#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
			#SBATCH --mail-user=username@uga.edu # Where to send mail

			cd $SLURM_SUBMIT_DIR

			ml BUSCO/5.8.3-foss-2023a # load BUSCO v5.8.3 module

			export AUGUSTUS_CONFIG_PATH=${PWD}/config_augustus
			export BUSCO_CONFIG_FILE=${PWD}/config.ini

			time busco --config ./config.ini --cpu 4 [options]
			</pre>

			where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.


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

	<pre class="gcommand">		<pre class="gcommand">
	~~[cft07037@b1-24 bin]$~~ ml BUSCO/5.5.0-foss-~~2022a~~		ml BUSCO/5.8.3-foss-2023a
	~~[cft07037@b1-24 bin]$~~ busco -h		busco -h
	usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]		usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]

	Welcome to BUSCO 5.5.0: the Benchmarking Universal Single-Copy Ortholog assessment tool.		Welcome to BUSCO 5.8.3: the Benchmarking Universal Single-Copy Ortholog assessment tool.
	For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO		For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO

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	Specify the name of the BUSCO lineage to be used.		Specify the name of the BUSCO lineage to be used.
	--augustus Use augustus gene predictor for eukaryote runs		--augustus Use augustus gene predictor for eukaryote runs
	--augustus_parameters --PARAM1=VALUE1,--PARAM2=VALUE2		--augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
	Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma.		Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
	--augustus_species AUGUSTUS_SPECIES		--augustus_species AUGUSTUS_SPECIES
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	--contig_break n Number of contiguous Ns to signify a break between contigs. Default is n=10.		--contig_break n Number of contiguous Ns to signify a break between contigs. Default is n=10.
	--datasets_version DATASETS_VERSION		--datasets_version DATASETS_VERSION
	Specify the version of BUSCO datasets, e.g. odb10		Specify the version of BUSCO datasets, e.g. odb10, odb12 (default odb12)
	--download [dataset ...]		--download [dataset ...]
	Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus". If used together with other command line arguments, make sure to place this last.		Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus". If used together with other command line arguments, make sure to place this last.
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	--list-datasets Print the list of available BUSCO datasets		--list-datasets Print the list of available BUSCO datasets
	--long Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms		--long Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms
			--metaeuk Use Metaeuk gene predictor
	--metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"		--metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
	Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.		Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
	--metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"		--metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
	Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.		Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
	--miniprot Use ~~miniprot~~ gene predictor for ~~eukaryote runs~~		--miniprot Use Miniprot gene predictor
			--skip_bbtools Skip BBTools for assembly statistics
	--offline To indicate that BUSCO cannot attempt to download files		--offline To indicate that BUSCO cannot attempt to download files
			--opt-out-run-stats Opt out of data collection. Information on the data collected is available in the user guide.
	--out_path OUTPUT_PATH		--out_path OUTPUT_PATH
	Optional location for results folder, excluding results folder name. Default is current working directory.		Optional location for results folder, excluding results folder name. Default is current working directory.
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	Writes ACGTN content per scaffold to a file scaffold_composition.txt		Writes ACGTN content per scaffold to a file scaffold_composition.txt
	--tar Compress some subdirectories with many files to save space		--tar Compress some subdirectories with many files to save space
	~~--update-data Download and replace with last versions all lineages datasets and files necessary to their automated selection~~
	-v, --version Show this version and exit		-v, --version Show this version and exit
	</pre>		</pre>

Moses: /* Version 5.8.2, Singularity Image */

2025-03-05T20:50:47Z

Version 5.8.2, Singularity Image

← Older revision		Revision as of 16:50, 5 March 2025
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	==== Version 5.8.2, Singularity Image ====		==== Version 5.8.2, Singularity Image ====

	* Version 4.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif		* Version 5.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif
	Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:		Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:

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	'''Example shell script''' sub.sh to run BUSCO/4.8.2 singularity container:		'''Example shell script''' sub.sh to run BUSCO/5.8.2 singularity container:

	<pre class="gscript">		<pre class="gscript">

Moses: /* Version 4.8.2, Singularity Image */

2025-03-05T20:49:29Z

Version 4.8.2, Singularity Image

← Older revision		Revision as of 16:49, 5 March 2025
Line 92:		Line 92:
	where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.		where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.

	==== Version 4.8.2, Singularity Image ====		==== Version 5.8.2, Singularity Image ====

	* Version 4.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif		* Version 4.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif

Moses: /* Version 5.5.0 */

2025-03-05T20:48:58Z

Version 5.5.0

← Older revision		Revision as of 16:48, 5 March 2025
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	export BUSCO_CONFIG_FILE=${PWD}/config.ini		export BUSCO_CONFIG_FILE=${PWD}/config.ini

	time ~~singularity~~ exec --bind ./config_augustus/:/augustus/config /apps/singularity-images/busco-4.0.5.~~simg run_busco~~ --config ./config.ini --cpu 4 [options]		time apptainer exec --bind ./config_augustus:/usr/share/augustus/config /apps/singularity-images/busco-5.8.2.sif busco --config ./config.ini --cpu 4 [options]
	</pre>		</pre>

Moses: /* Version 4.8.2, Singularity Image */

2025-03-05T20:45:47Z

Version 4.8.2, Singularity Image

← Older revision		Revision as of 16:45, 5 March 2025
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	* Version 4.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif		* Version 4.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif
	~~Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:~~

	Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:		Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:

	<pre class="gscript">		<pre class="gscript">
	cp -r /~~apps~~/eb/~~AUGUSTUS~~/~~3.3~~.~~3-foss-2019b~~/~~config~~ config_augustus		apptainer exec /apps/singularity-images/busco-5.8.2.sif cp -r /usr/share/augustus/config/ ./config_augustus
	export AUGUSTUS_CONFIG_PATH=config_augustus		export AUGUSTUS_CONFIG_PATH=config_augustus
	</pre>		</pre>
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	<pre class="gscript">		<pre class="gscript">
	~~singularity~~ exec /apps/singularity-images/busco-4.0.5.~~simg~~ cp /busco/config/config.ini .		apptainer exec /apps/singularity-images/busco-5.8.2.sif cp /busco-5.8.2/config/config.ini .
	vim config.ini		vim config.ini
	export BUSCO_CONFIG_FILE=config.ini		export BUSCO_CONFIG_FILE=config.ini
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	'''Example shell script''' sub.sh to run BUSCO/4.0.5 singularity container:		'''Example shell script''' sub.sh to run BUSCO/4.8.2 singularity container:

	<pre class="gscript">		<pre class="gscript">

Moses at 20:43, 5 March 2025

2025-03-05T20:43:32Z

← Older revision		Revision as of 16:43, 5 March 2025
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	Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:		Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:

			Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:

			<pre class="gscript">
			cp -r /apps/eb/AUGUSTUS/3.3.3-foss-2019b/config config_augustus
			export AUGUSTUS_CONFIG_PATH=config_augustus
			</pre>

			Please also copy the BUSCO config file config.ini from its singularity image to your current working folder and modify the input file value and other values as needed in it.

			<pre class="gscript">
			singularity exec /apps/singularity-images/busco-4.0.5.simg cp /busco/config/config.ini .
			vim config.ini
			export BUSCO_CONFIG_FILE=config.ini
			</pre>


			'''Example shell script''' sub.sh to run BUSCO/4.0.5 singularity container:

			<pre class="gscript">
			#!/bin/bash
			#SBATCH --job-name=busco # Job name
			#SBATCH --partition=batch # Partition (queue) name
			#SBATCH --ntasks=1 # Run a single task
			#SBATCH --cpus-per-task=4 # Number of CPU cores per task
			#SBATCH --mem=10gb # Job memory request
			#SBATCH --time=24:00:00 # Time limit hrs:min:sec
			#SBATCH --output=log.%j.out # Standard output log
			#SBATCH --error=log.%j.err # Standard error log
			#SBATCH --export=NONE # Don't export user's explicit env variables to compute node
			#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
			#SBATCH --mail-user=username@uga.edu # Where to send mail

			cd $SLURM_SUBMIT_DIR

			export AUGUSTUS_CONFIG_PATH=${PWD}/config_augustus
			export BUSCO_CONFIG_FILE=${PWD}/config.ini

			time singularity exec --bind ./config_augustus/:/augustus/config /apps/singularity-images/busco-4.0.5.simg run_busco --config ./config.ini --cpu 4 [options]
			</pre>

			where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.


			Here is an example of job submission command:
			<pre class="gcommand">
			sbatch sub.sh
			</pre>

	==== ersion 4.0.5, Singularity Image ====		==== ersion 4.0.5, Singularity Image ====

Moses at 20:42, 5 March 2025

2025-03-05T20:42:55Z

← Older revision		Revision as of 16:42, 5 March 2025
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	where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.		where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the time limit, maximum memory, number of cores, and the job name need to be modified appropriately as well.

			==== Version 4.8.2, Singularity Image ====

	==== ~~Version~~ 4.0.5, Singularity Image ====		* Version 4.8.2, is installed as a singularity image at /apps/singularity-images/busco-5.8.2.sif
			Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:


			==== ersion 4.0.5, Singularity Image ====

	* version 2.0 is installed as a singularity image at /apps/singularity-images/busco-2.0.simg		* version 2.0 is installed as a singularity image at /apps/singularity-images/busco-2.0.simg

Moses at 20:39, 5 March 2025

2025-03-05T20:39:10Z

@@ Line 64: / Line 64: @@
 export BUSCO_CONFIG_FILE=config.ini
 </pre>
 '''Example shell script''' sub.sh to run BUSCO/5.5.0 on the batch partition: