Bailey Carlson
# Load module
module load singularity/3.8.3
# Download docker file of TETools with all inset packages and versions
singularity pull dfam-tetools-latest.sif docker://dfam/tetools:latest
# RepeatModeler Version 2.0.5
# RepeatClassifier Version 2.0.5
# RepeatMasker version 4.1.6
# Shows the resources the job used
scontrol show job JOBIDAmphibalanus_amphitrite A.amphitrite GCA_019059575.1_NRLGWU_Aamphi_draft_genomic.fna.gz Balanus_glandula B.glandula GCA_030265075.1_ASM3026507v1_genomic.fna.gz Balanus_nubilus B.nubilus GCA_031763405.1_ASM3176340v1_genomic.fna.gz Chirona_hameri C.hameri GCA_036785665.1_qxChiHame1_p1.0_genomic.fna.gz Lepas_anatifera L.anatifera GCA_034440635.1_ASM3444063v1_genomic.fna.gz Pollicipes_pollicipes P.pollicipes GCA_011947565.3_Ppol_2.1_genomic.fna.gz Semibalanus_balanoides S.balanoides GCA_014673585.1_Sbal3.1_genomic.fna.gz Tetraclita_rubescens T.rubescens soon to uploaded to github
Replace in the full selection below organism with whatever species your working on and replace the genomic.fna.gz file with the correct genome file name for your species
mv 1.BuildDatabase_T.rubescens.sh 1.BuildDatabase_organism.sh
mv 1.BuildDatabase_T.rubescens.slurm 1.BuildDatabase_organism.slurm
mv 2.RepeatModeler_T.rubescens.sh 2.RepeatModeler_organism.sh
mv 2.RepeatModeler_T.rubescens.slurm 2.RepeatModeler_organism.slurm
mv 3.RepeatMasker_T.rubescens.sh 3.RepeatMasker_organism.sh
mv 3.RepeatMasker_T.rubescens.slurm 3.RepeatMasker_organism.slurm - Takes minutes
#!/bin/bash
#SBATCH -J 1.BuildDatabase_organism.batch # --job-name= Name for your job.
#SBATCH -N 1 # --nodes= Number of nodes to spread cores across - default is 1.
#SBATCH --mem-per-cpu 240G # the amount of memory per core to request in MB.
#SBATCH -t 0-00:10:00 # --time= Runtime in minutes. Default is 10 minutes.
#SBATCH -p test # --partition Partition to submit to the standard compute node.
#SBATCH -o slurm_1.BuildDatabase_organism_%j.out # --output= Standard out goes to this file.
#SBATCH -e slurm_1.BuildDatabase_organism_%j.err # Standard err goes to this file.
#SBATCH --mail-user [email protected] # this is the email for notifications.
#SBATCH --mail-type ALL # this specifies what events will be emailed.
# Load module
module load singularity/3.8.3
# Execute your processing script
/home/bcarlson4/data/CCGP/TETools/organism/1.BuildDatabase_organism.sh#!/bin/bash
# Assuming your files are in the current directory
dir="/home/bcarlson4/data/CCGP/TETools/organism"
TETools="/home/bcarlson4/local/TETools/dfam-tetools-latest.sif"
# Execute your processing script
singularity run --home $dir \
$TETools BuildDatabase \
-name organism genomic.fna.gz- For barnacles genomes ~550 Mb to 2.5 Gb this takes ~3 days and more fragmented and repeated genomes run longer overall.
- I strongly recommend only using 10 cores for this process because if you use more RepeatModeler will slow down tremendously.
- If you get a memory error and need to restart step 2 use -recoverDir and change run time and partition if need be.
- singularity run –home $dir $TETools RepeatModeler
–engine ncbi –threads 10 -database organism -recoverDir RM_folder
#!/bin/bash
#SBATCH -J 2.RepeatModeler_organism.batch # --job-name= Name for your job.
#SBATCH -N 1 # --nodes= Number of nodes to spread cores across - default is 1.
#SBATCH --ntasks=10 #number of cores per node
#SBATCH --mem-per-cpu 24G # the amount of memory per core to request in MB.
#SBATCH -t 3-00:00:00 # --time= Runtime in minutes. Default is 10 minutes.
#SBATCH -p long # --partition Partition to submit to the standard compute node.
#SBATCH -o slurm_2.RepeatModeler_organism_%j.out # --output= Standard out goes to this file.
#SBATCH -e slurm_2.RepeatModeler_organism_%j.err # Standard err goes to this file.
#SBATCH --mail-user [email protected] # this is the email for notifications.
#SBATCH --mail-type ALL # this specifies what events will be emailed.
# Load module
module load singularity/3.8.3
# Execute your processing script
/home/bcarlson4/data/CCGP/TETools/organism/2.RepeatModeler_organism.sh#!/bin/bash
# Assuming your files are in the current directory
dir="/home/bcarlson4/data/CCGP/TETools/organism"
TETools="/home/bcarlson4/local/TETools/dfam-tetools-latest.sif"
# Execute your processing script
singularity run --home $dir \
$TETools RepeatModeler \
--engine ncbi --threads 10 -database organism- Takes less than a day
#!/bin/bash
#SBATCH -J 3.RepeatMasker_organism.batch # --job-name= Name for your job.
#SBATCH -N 1 # --nodes= Number of nodes to spread cores across - default is 1.
#SBATCH --ntasks=10 #number of cores per node
#SBATCH --mem-per-cpu 24G # the amount of memory per core to request in MB.
#SBATCH -t 1-00:00:00 # --time= Runtime in minutes. Default is 10 minutes.
#SBATCH -p medium # --partition Partition to submit to the standard compute node.
#SBATCH -o slurm_3.RepeatMasker_organism_%j.out # --output= Standard out goes to this file.
#SBATCH -e slurm_3.RepeatMasker_organism_%j.err # Standard err goes to this file.
#SBATCH --mail-user [email protected] # this is the email for notifications.
#SBATCH --mail-type ALL # this specifies what events will be emailed.
# Load module
module load singularity/3.8.3
# Execute your processing script
/home/bcarlson4/data/CCGP/TETools/organism/3.RepeatMasker_organism.sh#!/bin/bash
# Assuming your files are in the current directory
dir="/home/bcarlson4/data/CCGP/TETools/organism"
TETools="/home/bcarlson4/local/TETools/dfam-tetools-latest.sif"
# Execute your processing script
singularity run --home $dir \
$TETools RepeatMasker \
-pa 5 --gff -lib RM_path/consensi.fa.classified \
genomic.fna.gz