BUSCO-Teaching

Category

Bioinformatics

Program On

Teaching

Version

3.0.2

Author / Distributor

BUSCO

Description

" Benchmarking sets of Universal Single-Copy Orthologs" More details are at BUSCO

Running Program

The last version of this application is at /usr/local/apps/gb/BUSCO/3.0.2

Bacteria and Eukaryot data sets are located at /usr/local/apps/gb/BUSCO/3.0.2.data

To use this version, please load the module with

ml BUSCO/3.0.2 

Before run the program, copy the config files and change the input file value and other needed values at config file config_augustus/config.ini

cp /usr/local/apps/eb/AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14/config config_augustus
export AUGUSTUS_CONFIG_PATH=config_augustus
cp -R /usr/local/apps/gb/busco/3.0.2/config/config.ini config_ini
vi config.ini
export BUSCO_CONFIG_FILE=config.ini

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_BUSCO
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BUSCO.%j.out
#SBATCH --error=BUSCO.%j.err

cd $SLURM_SUBMIT_DIR
ml BUSCO/3.0.2
python /usr/local/apps/gb/BUSCO/3.0.2/scripts/run_BUSCO.py [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml BUSCO/3.0.2 
python /usr/local/apps/gb/BUSCO/3.0.2/scripts/run_BUSCO.py  -h
usage: python BUSCO.py -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]

Welcome to BUSCO 3.0.2: 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.

optional arguments:
  -i FASTA FILE, --in FASTA FILE
                        Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.
  -c N, --cpu N         Specify the number (N=integer) of threads/cores to use.
  -o OUTPUT, --out OUTPUT
                        Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path
  -e N, --evalue N      E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)
  -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_path LINEAGE
                        Specify location of the BUSCO lineage data to be used.
                        Visit http://busco.ezlab.org for available lineages.
  -f, --force           Force rewriting of existing files. Must be used when output files with the provided name already exist.
  -r, --restart         Restart an uncompleted run. Not available for the protein mode
  -sp SPECIES, --species SPECIES
                        Name of existing Augustus species gene finding parameters. See Augustus documentation for available options.
  --augustus_parameters AUGUSTUS_PARAMETERS
                        Additional parameters for the fine-tuning of Augustus run. For the species, do not use this option.
                        Use single quotes as follow: '--param1=1 --param2=2', see Augustus documentation for available options.
  -t PATH, --tmp_path PATH
                        Where to store temporary files (Default: ./tmp/)
  --limit REGION_LIMIT  How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
  --long                Optimization mode Augustus self-training (Default: Off) adds considerably to the run time, but can improve results for some non-model organisms
  -q, --quiet           Disable the info logs, displays only errors
  -z, --tarzip          Tarzip the output folders likely to contain thousands of files
  --blast_single_core   Force tblastn to run on a single core and ignore the --cpu argument for this step only. Useful if inconsistencies when using multiple threads are noticed
  -v, --version         Show this version and exit
  -h, --help            Show this help message and exit

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Installation

Source code is obtained from BUSCO

System

64-bit Linux