After creating a subset of the cbai_genome_v1.0 of contigs >100bp yesterday (subset named cbai_genome_v1.01), I wanted to generate BUSCO scores for cbai_genome_v1.01. This is primarily just to keep info consistent on our Genomic Resources wiki, as I don’t expect these scores to differ at all from the cbai_genome_v1.0 BUSCO scores.
Analysis was run on Mox.
SBATCH script (GitHub):
#!/bin/bash
## Job Name
#SBATCH --job-name=cbai_genome_v1.01_busco
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=3-00:00:00
## 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 --chdir=/gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco
###################################################################################
# Script to generate BUSCO score(s) for genome(s).
# These variables need to be set by user
## Save working directory
wd=$(pwd)
# Genomes directory
genomes_dir=/gscratch/srlab/sam/data/C_bairdi/genomes
# Genomes array
genomes_array=(
"${genomes_dir}"/cbai_genome_v1.01.fasta \
)
## Input files and settings
busco_db=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9
augustus_species=fly
threads=28
# Programs associative array
declare -A programs_array
programs_array=(
[busco]="/gscratch/srlab/programs/busco-v3/scripts/run_BUSCO.py"
)
## Set program paths
augustus_bin=/gscratch/srlab/programs/Augustus-3.3.2/bin
augustus_orig_config_dir=/gscratch/srlab/programs/Augustus-3.3.2/config
augustus_scripts=/gscratch/srlab/programs/Augustus-3.3.2/scripts
blast_dir=/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin
hmm_dir=/gscratch/srlab/programs/hmmer-3.2.1/src
# Export Augustus variable
export PATH="${augustus_bin}:$PATH"
export PATH="${augustus_scripts}:$PATH"
## 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}"
# Copy BUSCO config file
cp ${busco_config_default} "${busco_config_ini}"
# 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}"
###################################################################################
# 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
for genome in "${!genomes_array[@]}"
do
# Remove path from genome using parameter substitution
genome_name="${genomes_array[$genome]##*/}"
## Augustus config directories
augustus_dir=${wd}/${genome_name}_augustus
augustus_config_dir=${augustus_dir}/config
export AUGUSTUS_CONFIG_PATH="${augustus_config_dir}"
# Make Augustus directory if it doesn't exist
if [ ! -d "${augustus_dir}" ]; then
mkdir --parents "${augustus_dir}"
fi
# Copy Augustus config directory
cp --preserve -r ${augustus_orig_config_dir} "${augustus_dir}"
# Run BUSCO/Augustus training
${programs_array[busco]} \
--in ${genomes_array[$genome]} \
--out ${genome_name} \
--lineage_path ${busco_db} \
--mode genome \
--cpu ${threads} \
--long \
--species ${augustus_species} \
--tarzip \
--augustus_parameters='--progress=true'
# Capture FastA checksums for verification
echo ""
echo "Generating checksum for ${genome_name}"
md5sum "${genomes_array[$genome]}" > "${genome_name}".checksum.md5
echo "Finished generating checksum for ${genome_name}"
echo ""
done
# Document programs in PATH (primarily for program version ID)
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log
# Capture program options
for program in "${!programs_array[@]}"
do
{
echo "Program options for ${program}: "
echo ""
${programs_array[$program]} --help
echo ""
echo ""
echo "----------------------------------------------"
echo ""
echo ""
} &>> program_options.log || true
doneRESULTS
As usual, very fast, ~1.5mins:
Output folder:
# 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/C_bairdi/genomes/cbai_genome_v1.01.fasta -o cbai_genome_v1.01.fasta -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/C_bairdi/genomes/cbai_genome_v1.01.fasta
# BUSCO was run in mode: genome
C:0.4%[S:0.3%,D:0.1%],F:0.2%,M:99.4%,n:978
4 Complete BUSCOs (C)
3 Complete and single-copy BUSCOs (S)
1 Complete and duplicated BUSCOs (D)
2 Fragmented BUSCOs (F)
972 Missing BUSCOs (M)
978 Total BUSCO groups searchedAs expected, no differences in BUSCO scores between cbai_genome_v1.0 and cbai_genome_v1.01. Will add info to Genomic Resources wiki.