BUSCO-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
2.0, 4.0.5, 5.4.7, 5.5.0
Author / Distributor
Description
"BUSCO - Benchmarking sets of Universal Single-Copy Orthologs." More details are at BUSCO
Running Program
Version 5.4.7
- Version 5.4.7, is installed at /apps/eb/BUSCO/5.4.7-foss-2022a
BLAST+ v2.13.0 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.
To use this version of BUSCO, please load the module with
ml BUSCO/5.4.7-foss-2022a
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:
cp -r /apps/eb/AUGUSTUS/3.5.0-foss-2022a/config config_augustus export AUGUSTUS_CONFIG_PATH=config_augustus cp /apps/eb/BUSCO/5.4.7-foss-2022a/config/config.ini config.ini vim config.ini export BUSCO_CONFIG_FILE=config.ini
Version 5.5.0
- Version 5.5.0, is installed at /apps/eb/BUSCO/5.5.0-foss-2022a
To use this version of BUSCO, please first load the module with
ml BUSCO/5.5.0-foss-2022a
BLAST+ v2.13.0 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:
cp -r /apps/eb/AUGUSTUS/3.5.0-foss-2022a/config config_augustus export AUGUSTUS_CONFIG_PATH=config_augustus cp /apps/eb/BUSCO/5.5.0-foss-2022a/config/config.ini config.ini vim config.ini export BUSCO_CONFIG_FILE=config.ini
Example shell script sub.sh to run BUSCO/5.5.0 on the batch partition:
#!/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 $SLURM_SUBMIT_DIR
ml BUSCO/5.5.0-foss-2022a # load BUSCO v5.5.0 module
export AUGUSTUS_CONFIG_PATH=${PWD}/config_augustus
export BUSCO_CONFIG_FILE=${PWD}/config.ini
time busco --config ./config.ini --cpu 4 [options]
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 4.0.5, Singularity Image
- 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, is installed as a singularity image at /apps/singularity-images/busco-4.0.5.simg
To run this singularity image:
singularity exec /apps/singularity-images/busco-4.0.5.simg run_busco [options]
To get busco help info:
singularity exec /apps/singularity-images/busco-4.0.5.simg run_busco -h
To check busco version info:
singularity exec /apps/singularity-images/busco-4.0.5.simg run_busco -v
To have a check on other programs included in this busco singularity image:
singularity exec /apps/singularity-images/busco-4.0.5.simg ls /usr/local/bin singularity exec /apps/singularity-images/busco-4.0.5.simg ls /augustus singularity exec /apps/singularity-images/busco-4.0.5.simg ls /ncbi-blast-2.2.31+/bin singularity exec /apps/singularity-images/busco-4.0.5.simg ls /hmmer-3.2.1 singularity exec /apps/singularity-images/busco-4.0.5.simg ls /prodigal
Before run busco singularity container, please copy AUGUSTUS config folder to your current working folder:
cp -r /apps/eb/AUGUSTUS/3.3.3-foss-2019b/config config_augustus export AUGUSTUS_CONFIG_PATH=config_augustus
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.
singularity exec /apps/singularity-images/busco-4.0.5.simg cp /busco/config/config.ini . vim config.ini export BUSCO_CONFIG_FILE=config.ini
Example shell script sub.sh to run BUSCO/4.0.5 singularity container:
#!/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=${PWD}/config.ini
time singularity exec --bind ./config_augustus/:/augustus/config /apps/singularity-images/busco-4.0.5.simg run_busco --config ./config.ini --cpu 4 [options]
where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.
Here is an example of job submission command:
sbatch sub.sh
Documentation
[cft07037@b1-24 bin]$ ml BUSCO/5.5.0-foss-2022a
[cft07037@b1-24 bin]$ busco -h
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.
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
optional arguments:
-i SEQUENCE_FILE, --in SEQUENCE_FILE
Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.
-o OUTPUT, --out OUTPUT
Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. The path to the output folder is set with --out_path.
-m MODE, --mode MODE Specify which BUSCO analysis mode to run.
There are three valid modes:
- geno or genome, for genome assemblies (DNA)
- tran or transcriptome, for transcriptome assemblies (DNA)
- prot or proteins, for annotated gene sets (protein)
-l LINEAGE, --lineage_dataset LINEAGE
Specify the name of the BUSCO lineage to be used.
--augustus Use augustus gene predictor for eukaryote runs
--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.
--augustus_species AUGUSTUS_SPECIES
Specify a species for Augustus training.
--auto-lineage Run auto-lineage to find optimum lineage path
--auto-lineage-euk Run auto-placement just on eukaryote tree to find optimum lineage path
--auto-lineage-prok Run auto-lineage just on non-eukaryote trees to find optimum lineage path
-c N, --cpu N Specify the number (N=integer) of threads/cores to use.
--config CONFIG_FILE Provide a config file
--contig_break n Number of contiguous Ns to signify a break between contigs. Default is n=10.
--datasets_version DATASETS_VERSION
Specify the version of BUSCO datasets, e.g. odb10
--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_base_url DOWNLOAD_BASE_URL
Set the url to the remote BUSCO dataset location
--download_path DOWNLOAD_PATH
Specify local filepath for storing BUSCO dataset downloads
-e N, --evalue N E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)
-f, --force Force rewriting of existing files. Must be used when output files with the provided name already exist.
-h, --help Show this help message and exit
--limit N How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
--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
--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.
--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.
--miniprot Use miniprot gene predictor for eukaryote runs
--offline To indicate that BUSCO cannot attempt to download files
--out_path OUTPUT_PATH
Optional location for results folder, excluding results folder name. Default is current working directory.
-q, --quiet Disable the info logs, displays only errors
-r, --restart Continue a run that had already partially completed.
--scaffold_composition
Writes ACGTN content per scaffold to a file scaffold_composition.txt
--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
Installation
Source code is obtained from BUSCO
System
64-bit Linux