Genome Assessment - BUSCO Metazoa on Pgenerosa_v70 on Mox

2019
Geoduck Genome Sequencing
Author

Sam White

Published

July 10, 2019

Ran BUSCO on Mox for our Pgenerosa_v70 genome assembly to assess “completeness”.

SBATCH script (GitHub):

#!/bin/bash
## Job Name
#SBATCH --job-name=busco_pgen70
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=15-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070

# Load Python Mox module for Python module availability
module load intel-python3_2017

# Load Open MPI module for parallel, multi-node processing
module load icc_19-ompi_3.1.2

# SegFault fix?
export THREADS_DAEMON_MODEL=1

# Document programs in PATH (primarily for program version ID)
date >> system_path.log
echo "" >> system_path.log
echo "System PATH for $SLURM_JOB_ID" >> system_path.log
echo "" >> system_path.log
printf "%0.s-" {1..10} >> system_path.log
echo "${PATH}" | tr : \\n >> system_path.log


# Establish variables for more readable code

## Input files and settings
base_name=Pgenerosa_v070
busco_db=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9
genome_fasta=/gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v070.fa
augustus_species=fly
threads=28

## Save working directory
wd=$(pwd)

## Set program paths
augustus_bin=/gscratch/srlab/programs/Augustus-3.3.2/bin
augustus_scripts=/gscratch/srlab/programs/Augustus-3.3.2/scripts
blast_dir=/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin
busco=/gscratch/srlab/programs/busco-v3/scripts/run_BUSCO.py
hmm_dir=/gscratch/srlab/programs/hmmer-3.2.1/src

## Augustus configs
augustus_dir=${wd}/augustus
augustus_config_dir=${augustus_dir}/config
augustus_orig_config_dir=/gscratch/srlab/programs/Augustus-3.3.2/config

## BUSCO configs
busco_config_default=/gscratch/srlab/programs/busco-v3/config/config.ini.default
busco_config_ini=${wd}/config.ini

# Export BUSCO config file location
export BUSCO_CONFIG_FILE="${busco_config_ini}"

# Export Augustus variable
export PATH="${augustus_bin}:$PATH"
export PATH="${augustus_scripts}:$PATH"
export AUGUSTUS_CONFIG_PATH="${augustus_config_dir}"


# Copy BUSCO config file
cp ${busco_config_default} "${busco_config_ini}"

# Make Augustus directory if it doesn't exist
if [ ! -d "${augustus_dir}" ]; then
  mkdir --parents "${augustus_dir}"
fi

# Copy Augustus config directory
cp --preserve -r ${augustus_orig_config_dir} "${augustus_dir}"

# Edit BUSCO config file
## Set paths to various programs
### The use of the % symbol sets the delimiter sed uses for arguments.
### Normally, the delimiter that most examples use is a slash "/".
### But, we need to expand the variables into a full path with slashes, which screws up sed.
### Thus, the use of % symbol instead (it could be any character that is NOT present in the expanded variable; doesn't have to be "%").
sed -i "/^;cpu/ s/1/${threads}/" "${busco_config_ini}"
sed -i "/^tblastn_path/ s%tblastn_path = /usr/bin/%path = ${blast_dir}%" "${busco_config_ini}"
sed -i "/^makeblastdb_path/ s%makeblastdb_path = /usr/bin/%path = ${blast_dir}%" "${busco_config_ini}"
sed -i "/^augustus_path/ s%augustus_path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/%path = ${augustus_bin}%" "${busco_config_ini}"
sed -i "/^etraining_path/ s%etraining_path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/%path = ${augustus_bin}%" "${busco_config_ini}"
sed -i "/^gff2gbSmallDNA_path/ s%gff2gbSmallDNA_path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/%path = ${augustus_scripts}%" "${busco_config_ini}"
sed -i "/^new_species_path/ s%new_species_path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/%path = ${augustus_scripts}%" "${busco_config_ini}"
sed -i "/^optimize_augustus_path/ s%optimize_augustus_path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/%path = ${augustus_scripts}%" "${busco_config_ini}"
sed -i "/^hmmsearch_path/ s%hmmsearch_path = /home/osboxes/BUSCOVM/hmmer/hmmer-3.1b2-linux-intel-ia32/binaries/%path = ${hmm_dir}%" "${busco_config_ini}"


# Run BUSCO/Augustus training
${busco} \
--in ${genome_fasta} \
--out ${base_name} \
--lineage_path ${busco_db} \
--mode genome \
--cpu ${threads} \
--long \
--species ${augustus_species} \
--tarzip \
--augustus_parameters='--progress=true'

RESULTS

This took ~15hrs to run:

BUSCO runtime screencap

Output folder:

BUSCO scores:

# BUSCO version is: 3.0.2
# The lineage dataset is: metazoa_odb9 (Creation date: 2016-02-13, number of species: 65, number of BUSCOs: 978)
# To reproduce this run: python /gscratch/srlab/programs/busco-v3/scripts/run_BUSCO.py -i /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v070.fa -o Pgenerosa_v070 -l /gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/ -m genome -c 28 --long -z -sp fly --augustus_parameters '--progress=true'
#
# Summarized benchmarking in BUSCO notation for file /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v070.fa
# BUSCO was run in mode: genome

    C:84.2%[S:78.5%,D:5.7%],F:9.4%,M:6.4%,n:978

    824 Complete BUSCOs (C)
    768 Complete and single-copy BUSCOs (S)
    56  Complete and duplicated BUSCOs (D)
    92  Fragmented BUSCOs (F)
    62  Missing BUSCOs (M)
    978 Total BUSCO groups searched