08_BINNING

CONCOCT, METABAT2, MAXBIN2, and DASTOOL.

first three done on SAGA, dastool used on kjempefuru when the driver wouldn't function properly without more resources I couldn't figure out how to properly allocate.

#!/usr/bin/bash
# every job must be accounted for
#SBATCH --account=nn9836k
#SBATCH --job-name=14ROV7-D

# every job requires some specification of the number of cores to be used
#SBATCH --ntasks=1
# every job requires some specification of the memory (RAM) it needs
#SBATCH --cpus-per-task=20
#SBATCH --mem-per-cpu=5G
# every job requires a runtime limit
#SBATCH --time=10:00:00

# setting up software environment
module purge

# load the conda version
module load Miniconda3/4.9.2

# Set the ${PS1} (needed in the source of the Anaconda environment)
export PS1=\$

# Source the conda environment setup
# The variable ${EBROOTANACONDA3} or ${EBROOTMINICONDA3}
# So use one of the following lines
# comes with the module load command
# source ${EBROOTANACONDA3}/etc/profile.d/conda.sh
source ${EBROOTMINICONDA3}/etc/profile.d/conda.sh

# Deactivate any spill-over environment from the login node
conda deactivate &>/dev/null

# Activate the environment by using the full path (not name)
# to the environment. The full path is listed if you do
# conda info --envs at the command prompt.
conda activate /cluster/projects/nn9836k/conda_envs/anvio

# set up paths

ASSEMBLY_PATH="/cluster/projects/nn9836k/Metagenomics_AMOR_2020/04_CONTIGS"
MERGED_PROFILE_PATH="/cluster/projects/nn9836k/Metagenomics_AMOR_2020/07_MERGED_PROFILES"


anvi-cluster-contigs -c ${ASSEMBLY_PATH}/14ROV7-D/14ROV7-D.prefixed.contigs.db -p ${MERGED_PROFILE_PATH}/14ROV7-D-MERGED-PROFILE/PROFILE.db -C concoct -T 20 --driver concoct --just-do-it; anvi-cluster-contigs -c ${ASSEMBLY_PATH}/14ROV7-D/14ROV7-D.prefixed.contigs.db -p ${MERGED_PROFILE_PATH}/14ROV7-D-MERGED-PROFILE/PROFILE.db -C metabat2 -T 20 --driver metabat2 --just-do-it; anvi-cluster-contigs -c ${ASSEMBLY_PATH}/14ROV7-D/14ROV7-D.prefixed.contigs.db -p ${MERGED_PROFILE_PATH}/14ROV7-D-MERGED-PROFILE/PROFILE.db -C maxbin2 -T 20 --driver maxbin2 --just-do-it
(base) [ede041@login-3.SAGA /cluster/projects/nn9836k/Metagenomics_AMOR_2020/08_BINNING]$ head -1000 binning_temp.sh 
#!/usr/bin/bash
# every job must be accounted for
#SBATCH --account=nn9836k
#SBATCH --job-name=<assembly>

# every job requires some specification of the number of cores to be used
#SBATCH --ntasks=1
# every job requires some specification of the memory (RAM) it needs
#SBATCH --cpus-per-task=20
#SBATCH --mem-per-cpu=5G
# every job requires a runtime limit
#SBATCH --time=10:00:00

# setting up software environment
module purge

# load the conda version
module load Miniconda3/4.9.2

# Set the ${PS1} (needed in the source of the Anaconda environment)
export PS1=\$

# Source the conda environment setup
# The variable ${EBROOTANACONDA3} or ${EBROOTMINICONDA3}
# So use one of the following lines
# comes with the module load command
# source ${EBROOTANACONDA3}/etc/profile.d/conda.sh
source ${EBROOTMINICONDA3}/etc/profile.d/conda.sh

# Deactivate any spill-over environment from the login node
conda deactivate &>/dev/null

# Activate the environment by using the full path (not name)
# to the environment. The full path is listed if you do
# conda info --envs at the command prompt.
conda activate /cluster/projects/nn9836k/conda_envs/anvio

# set up paths

ASSEMBLY_PATH="/cluster/projects/nn9836k/Metagenomics_AMOR_2020/04_CONTIGS"
MERGED_PROFILE_PATH="/cluster/projects/nn9836k/Metagenomics_AMOR_2020/07_MERGED_PROFILES"


anvi-cluster-contigs -c ${ASSEMBLY_PATH}/<assembly>/<assembly>.prefixed.contigs.db -p ${MERGED_PROFILE_PATH}/<assembly>-MERGED-PROFILE/PROFILE.db -C concoct -T 20 --driver concoct --just-do-it; anvi-cluster-contigs -c ${ASSEMBLY_PATH}/<assembly>/<assembly>.prefixed.contigs.db -p ${MERGED_PROFILE_PATH}/<assembly>-MERGED-PROFILE/PROFILE.db -C metabat2 -T 20 --driver metabat2 --just-do-it; anvi-cluster-contigs -c ${ASSEMBLY_PATH}/<assembly>/<assembly>.prefixed.contigs.db -p ${MERGED_PROFILE_PATH}/<assembly>-MERGED-PROFILE/PROFILE.db -C maxbin2 -T 20 --driver maxbin2 --just-do-it