Continuing to try to identify the best C.bairdi transcriptome, we decided to extract all non-dinoflagellate sequences from cbai_transcriptome_v2.0 (RNAseq shorthand: 2018, 2019, 2020-GW, 2020-UW) and cbai_transcriptome_v3.0 (RNAseq shorthand: 2018, 2019, 2020-UW).
Now, want to assess its cbai_transcriptome_v3.1 “completeness” using BUSCO and the metazoa_odb9 database.
BUSCO was run with the --mode transcriptome option on Mox.
SBATCH script (GitHub):
#!/bin/bash
## Job Name
#SBATCH --job-name=cbai_busco_v3.1_transcriptome
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=1-00:00:00
## 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/20200605_cbai_busco_transcriptome_v3.1
### C.bairdi transcriptome assembly completeness assessment using BUSCO.
### This is checking cbai_transcriptome_v1.7.fasta
# 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
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log
## Input files and settings
busco_db=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9
transcriptome_fasta=/gscratch/srlab/sam/data/C_bairdi/transcriptomes/cbai_transcriptome_v3.1.fasta
augustus_species=fly
threads=28
## Save working directory
wd=$(pwd)
# Extract FastA filename
fasta_name=${transcriptome_fasta##*/}
## 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 ${transcriptome_fasta} \
--out ${fasta_name} \
--lineage_path ${busco_db} \
--mode transcriptome \
--cpu ${threads} \
--long \
--species ${augustus_species} \
--tarzip \
--augustus_parameters='--progress=true'
# Create checksum for potential verification
md5sum "${transcriptome_fasta}" >> "${fasta_name}".checksum.md5RESULTS
As always, very quick; ~4.5mins:
Output folder:
Short summary file (text):
# 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/transcriptomes/cbai_transcriptome_v3.1.fasta -o cbai_transcriptome_v3.1.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/C_bairdi/transcriptomes/cbai_transcriptome_v3.1.fasta
# BUSCO was run in mode: transcriptome
C:96.5%[S:40.3%,D:56.2%],F:2.2%,M:1.3%,n:978
944 Complete BUSCOs (C)
394 Complete and single-copy BUSCOs (S)
550 Complete and duplicated BUSCOs (D)
22 Fragmented BUSCOs (F)
12 Missing BUSCOs (M)
978 Total BUSCO groups searchedWill add scores to Genomic Resources wiki. Also, after running BUSCO on the cbai_transcriptome_v3.1 transcriptome, I will update my BUSCO comparision notebook entry from 20200528.