BUSCO: Difference between revisions
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It is an application for assessing genome assembly and annotation completeness. | It is an application for assessing genome assembly and annotation completeness. | ||
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For more information, see the [https://busco.ezlab.org/busco_userguide.html user manual]. | For more information, see the [https://busco.ezlab.org/busco_userguide.html user manual]. | ||
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To see the latest available version, run: | To see the latest available version, run: | ||
{{Command|avail_wheel busco}} | {{Command|avail_wheel busco}} | ||
== Python Wheel == | == Python Wheel == <!--T:18--> | ||
=== Installation === | === Installation === | ||
'''1.''' Load the necessary modules: | '''1.''' Load the necessary modules: | ||
{{Command|module load StdEnv/2020 gcc python augustus hmmer blast+ metaeuk prodigal r}} | {{Command|module load StdEnv/2020 gcc python augustus hmmer blast+ metaeuk prodigal r}} | ||
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'''2.''' Create the virtual environment: | '''2.''' Create the virtual environment: | ||
{{Commands | {{Commands | ||
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}} | }} | ||
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'''3.''' Install the wheel and its dependencies: | '''3.''' Install the wheel and its dependencies: | ||
{{Command | {{Command | ||
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}} | }} | ||
=== Usage === | === Usage === <!--T:21--> | ||
==== Datasets ==== | ==== Datasets ==== | ||
You must pre-download any datasets from [https://busco-data.ezlab.org/v5/data/ busco data] before submitting your job. | You must pre-download any datasets from [https://busco-data.ezlab.org/v5/data/ busco data] before submitting your job. | ||
==== Test ==== | ==== Test ==== <!--T:22--> | ||
'''4.''' Download test data: | '''4.''' Download test data: | ||
{{Commands | {{Commands | ||
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}} | }} | ||
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'''5.''' Run: | '''5.''' Run: | ||
{{Command|busco --offline --in genome.fna --out TEST --lineage_dataset bacteria_odb10 --mode genome --cpu ${SLURM_CPUS_PER_TASK-1} }} | {{Command|busco --offline --in genome.fna --out TEST --lineage_dataset bacteria_odb10 --mode genome --cpu ${SLURM_CPUS_PER_TASK-1} }} | ||
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The command should take less than 60 seconds to complete. Production runs which take longer must be submitted to the [[Running jobs|scheduler]]. | The command should take less than 60 seconds to complete. Production runs which take longer must be submitted to the [[Running jobs|scheduler]]. | ||
=== Slurm tips === | === Slurm tips === <!--T:25--> | ||
Specify <tt>--offline</tt> to avoid using internet. | Specify <tt>--offline</tt> to avoid using internet. | ||
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Specify <tt>--cpu</tt> to <tt>$SLURM_CPUS_PER_TASK</tt> in your job submission script to use the number of cpus allocated. | Specify <tt>--cpu</tt> to <tt>$SLURM_CPUS_PER_TASK</tt> in your job submission script to use the number of cpus allocated. | ||
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Specify <tt>--restart</tt> to restart from a partial run. | Specify <tt>--restart</tt> to restart from a partial run. | ||
Revision as of 00:07, 30 March 2021
BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs".
It is an application for assessing genome assembly and annotation completeness.
For more information, see the user manual.
Available versions
Recent versions are available as wheels. Older version is available as a module, please see the module section below.
To see the latest available version, run:
[name@server ~]$ avail_wheel busco
Python Wheel
Installation
1. Load the necessary modules:
[name@server ~]$ module load StdEnv/2020 gcc python augustus hmmer blast+ metaeuk prodigal r
2. Create the virtual environment:
[name@server ~]$ virtualenv busco_env
[name@server ~]$ source busco_env/bin/activate
3. Install the wheel and its dependencies:
(busco_env) $ pip install biopython pandas busco --no-index
Usage
Datasets
You must pre-download any datasets from busco data before submitting your job.
Test
4. Download test data:
[name@server ~]$ wget https://gitlab.com/ezlab/busco/-/raw/master/test_data/bacteria/genome.fna
[name@server ~]$ wget https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz
5. Run:
[name@server ~]$ busco --offline --in genome.fna --out TEST --lineage_dataset bacteria_odb10 --mode genome --cpu ${SLURM_CPUS_PER_TASK-1}
The command should take less than 60 seconds to complete. Production runs which take longer must be submitted to the scheduler.
Slurm tips
Specify --offline to avoid using internet.
Specify --cpu to $SLURM_CPUS_PER_TASK in your job submission script to use the number of cpus allocated.
Specify --restart to restart from a partial run.
Module
1. Load the necessary modules:
[name@server ~]$ module load StdEnv/2018.3 gcc/7.3.0 openmpi/3.1.4 busco/3.0.2 r/4.0.2
This will also load modules for augustus, blast+, hmmer and some other
software packages that BUSCO relies upon.
2. Copy the configuration file:
[name@server ~]$ cp -v $EBROOTBUSCO/config/config.ini.default $HOME/busco_config.ini
or
[name@server ~]$ wget -O $HOME/busco_config.ini https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default
3. Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below:
[tblastn]
# path to tblastn
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/blast+/2.7.1/bin/
[makeblastdb]
# path to makeblastdb
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/blast+/2.7.1/bin/
[augustus]
# path to augustus
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/bin/
[etraining]
# path to augustus etraining
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/bin/
# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/
[new_species.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/
[optimize_augustus.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/
[hmmsearch]
# path to HMMsearch executable
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/hmmer/3.1b2/bin/
[Rscript]
# path to Rscript, if you wish to use the plot tool
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/r/4.0.2/bin/
4. Copy the Augustus config directory to a writable location:
[name@server ~]$ cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config
5. Check that it runs.
[name@server ~]$ export BUSCO_CONFIG_FILE=$HOME/busco_config.ini
[name@server ~]$ export AUGUSTUS_CONFIG_PATH=$HOME/augustus_config
[name@server ~]$ run_BUSCO.py --in $EBROOTBUSCO/sample_data/target.fa --out TEST --lineage_path $EBROOTBUSCO/sample_data/example --mode genome
The run_BUSCO.py command should take less than 60 seconds to complete.
Production runs which take longer should be submitted to the scheduler.
Troubleshooting
Cannot write to Augustus config path
Make sure you have copied the config directory to a writable location and exported the AUGUSTUS_CONFIG_PATH variable.