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03b_funannotate_prep_assembly_JL201.sb
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03b_funannotate_prep_assembly_JL201.sb
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#!/bin/bash --login
########## Define Resources Needed with SBATCH Lines ##########
#SBATCH --time=00:10:00 # limit of wall clock time - how long the job will run (same as -t)
#SBATCH --ntasks=1 # number of tasks - how many tasks (nodes) that you require (same as -n)
#SBATCH --cpus-per-task=1 # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem=10G # memory required per node - amount of memory (in bytes)
#SBATCH --job-name=funannotate_prep_JL201 # you can give your job a name for easier identification (same as -J)
#SBATCH --output=%x-%j.SLURMout
########## Command Lines to Run ##########
## Prep assemblies
conda activate aaftf
module load GCC/10.2.0 OpenMPI/4.0.5 AUGUSTUS/3.4.0 DIAMOND hisat2/2.1.0 icc/2018.1.163-GCC-6.4.0-2.28 impi/2018.1.163 SAMtools/1.8 PASA/2.4.1 Trinity/2.8.4 kallisto/0.46.0 FASTA/36.3.8h_04-May-2020
cd /mnt/scratch/liberjul/Yeast_genomes/funannotate_working_dir
DATADIR=~/He_Lab/Yeast_genomes/data
funannotate clean -i $DATADIR/assembly/JL201/scaffolds.fasta \
-o $DATADIR/assembly/JL201/scaffolds.clean.fasta
funannotate sort -i $DATADIR/assembly/JL201/scaffolds.clean.fasta \
-o $DATADIR/assembly/JL201/scaffolds.sorted.fasta
funannotate mask -i $DATADIR/assembly/JL201/scaffolds.sorted.fasta \
-o $DATADIR/assembly/JL201/scaffolds.masked.fasta
conda deactivate
scontrol show job $SLURM_JOB_ID ### write job information to output file