--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left layout: post title: Genome Assessment - BUSCO Metazoa on Pgenerosa_v074 on Mox date: '2019-07-10 15:19' tags: - busco - metazoa - Pgenerosa_v074 - v074 - Panopea generosa - geoduck - mox categories: - 2019 - Geoduck Genome Sequencing --- Ran BUSCO on Mox for our [Pgenerosa_v74 genome assembly](https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome-2) to assess "completeness". This is the assembly that only has the longest 18 scaffolds (the scaffolds hand-curated by Phase Genomics). SBATCH script (GitHub): - [20190710_busco_pgen_v074_unannotated.sh](https://github.com/RobertsLab/sams-notebook/blob/master/sbatch_scripts/20190710_busco_pgen_v074_unannotated.sh) ```shell #!/bin/bash ## Job Name #SBATCH --job-name=busco_pgen74 ## 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_v074_unannotated # 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_v074 busco_db=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9 genome_fasta=/gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v074.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 ~12hrs to run: ![BUSCO runtime screencap](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20190710_busco_pgen74_runtime.png?raw=true) Output folder: - [20190710_busco_pgen_v074_unannotated](https://gannet.fish.washington.edu/Atumefaciens/20190710_busco_pgen_v074_unannotated) BUSCO scores: - [20190710_busco_pgen_v074_unannotated/run_Pgenerosa_v074/short_summary_Pgenerosa_v074.txt](https://gannet.fish.washington.edu/Atumefaciens/20190710_busco_pgen_v074_unannotated/run_Pgenerosa_v074/short_summary_Pgenerosa_v074.txt) ``` # 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_v074.fa -o Pgenerosa_v074 -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_v074.fa # BUSCO was run in mode: genome C:71.6%[S:70.7%,D:0.9%],F:4.7%,M:23.7%,n:978 700 Complete BUSCOs (C) 691 Complete and single-copy BUSCOs (S) 9 Complete and duplicated BUSCOs (D) 46 Fragmented BUSCOs (F) 232 Missing BUSCOs (M) 978 Total BUSCO groups searched ```