BUSCO-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.0, 4.0.5, 5.4.7, 5.5.0

Author / Distributor

BUSCO

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

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Installation

Source code is obtained from BUSCO

System

64-bit Linux