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 ${MERGED_PROFILE_PATH}/14ROV7-D-MERGED-PROFILE/PROF(base) [ede041@(ba(ba(base) [ede0(ba(ba(ba(ba(ba(base) [e(base) [e(base) [e(base)(base)(base) [e(base)(base) [e(base) [e(base) [e(base)(base)(ba(base)(ba(ba(base)(ba(base) [ede041@login-3.SAGA /cluster/projects/nn9836k/Metagenomics_AMOR_2020/08_BINNING]$ head -1000 binning_14ROV7-D.sh #!/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 ´´´