Grace was recently working on writing up a manuscript which did a basic comparison of our C.bairdi transcriptome (cbai_transcriptome_v3.1) (see the Genomic Resources wiki for more deets) to two other species’ transcriptome assemblies. We wanted BUSCO evaluations as part of this comparison, but the two other species did not have BUSCO scores in their respective publications. As such, I decided to generate them myself, as BUSCO runs very quickly. The job was run on Mox.
Info on the other two species’ transcriptomes:
-
Carcinus maenas (green crab) transcriptome: NCBI TSA
-
Litopenaeus vannamei (whiteleg shrimp) transcriptome: OAKTrust
SBATCH script (GitHub):
#!/bin/bash
## Job Name
#SBATCH --job-name=20201110_crustacean-transcriptomes_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=200G
##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/20201110_crustacean-transcriptomes_busco
###################################################################################
# These variables need to be set by user
## Save working directory
wd=$(pwd)
# Transcriptomes array
transcriptomes_array=(
/gscratch/srlab/sam/data/C_maenas/transcriptomes/GBXE01.1.fsa_nt \
/gscratch/srlab/sam/data/L_vannamei/transcriptomes/Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta
)
## Input files and settings
busco_db=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9
augustus_species=fly
threads=28
# Programs associative array
declare -A programs_array
programs_array=(
[busco]="/gscratch/srlab/programs/busco-v3/scripts/run_BUSCO.py"
)
## Set program paths
augustus_bin=/gscratch/srlab/programs/Augustus-3.3.2/bin
augustus_orig_config_dir=/gscratch/srlab/programs/Augustus-3.3.2/config
augustus_scripts=/gscratch/srlab/programs/Augustus-3.3.2/scripts
blast_dir=/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin/
hmm_dir=/gscratch/srlab/programs/hmmer-3.2.1/src/
# Export Augustus variable
export PATH="${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 transcriptome in "${!transcriptomes_array[@]}"
do
# Remove path from transcriptome using parameter substitution
transcriptome_name="${transcriptomes_array[$transcriptome]##*/}"
## Augustus config directories
augustus_dir=${wd}/${transcriptome_name}_augustus
augustus_config_dir=${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 ${transcriptomes_array[$transcriptome]} \
--out ${transcriptome_name} \
--lineage_path ${busco_db} \
--mode transcriptome \
--cpu ${threads} \
--long \
--species ${augustus_species} \
--tarzip \
--augustus_parameters='--progress=true'
# Capture FastA checksums for verification
echo ""
echo "Generating checksum for ${transcriptome_name}"
md5sum "${transcriptomes_array[$transcriptome]}" > "${transcriptome_name}".checksum.md5
echo "Finished generating checksum for ${transcriptome_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
done
RESULTS
As usual, runtime was very quick ~8mins:
Output folder:
C.maenas
# 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_maenas/transcriptomes/GBXE01.1.fsa_nt -o GBXE01.1.fsa_nt -l /gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/ -m transcriptome -c 28 --long -z
#
# Summarized benchmarking in BUSCO notation for file /gscratch/srlab/sam/data/C_maenas/transcriptomes/GBXE01.1.fsa_nt
# BUSCO was run in mode: transcriptome
C:95.7%[S:57.0%,D:38.7%],F:3.6%,M:0.7%,n:978
935 Complete BUSCOs (C)
557 Complete and single-copy BUSCOs (S)
378 Complete and duplicated BUSCOs (D)
35 Fragmented BUSCOs (F)
8 Missing BUSCOs (M)
978 Total BUSCO groups searched
L.vannamei
# 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/L_vannamei/transcriptomes/Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta -o Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta -l /gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/ -m transcriptome -c 28 --long -z
#
# Summarized benchmarking in BUSCO notation for file /gscratch/srlab/sam/data/L_vannamei/transcriptomes/Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta
# BUSCO was run in mode: transcriptome
C:98.1%[S:72.7%,D:25.4%],F:0.9%,M:1.0%,n:978
959 Complete BUSCOs (C)
711 Complete and single-copy BUSCOs (S)
248 Complete and duplicated BUSCOs (D)
9 Fragmented BUSCOs (F)
10 Missing BUSCOs (M)
978 Total BUSCO groups searched