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04b_funannotate_predict_JL221_NP11_proteins.sb
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04b_funannotate_predict_JL221_NP11_proteins.sb
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#!/bin/bash --login
########## Define Resources Needed with SBATCH Lines ##########
#SBATCH --time=08:00:00 # 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=16 # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem=32G # memory required per node - amount of memory (in bytes)
#SBATCH --job-name=funannotate_predict_JL221_NP11_prot # you can give your job a name for easier identification (same as -J)
#SBATCH --output=%x-%j.SLURMout
########## Command Lines to Run ##########
## Prep assemblies
export QUARRY_PATH=~/bin/CodingQuarry_v2.0/QuarryFiles
export ZOE=~/bin/SNAP/Zoe
# export AUGUSTUS_CONFIG_PATH=~/bin/anaconda3/envs/aaftf/config/
#FUNANNOTATE_DB and GENEMARK_PATH are specified in ~/.bashrc
#GlimmerHMM and SNAP are added to the path in ~/.bashrc
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
export AUGUSTUS_CONFIG_PATH=~/bin/anaconda3/envs/aaftf/config/
cd /mnt/scratch/liberjul/Yeast_genomes/funannotate_working_dir
DATADIR=~/He_Lab/Yeast_genomes/data
~/bin/gmes_linux_64/gmes_petap.pl --ES --max_intron 3000 --soft_mask 2000 --cores 16 \
--sequence $DATADIR/assembly/JL221/scaffolds.masked.fasta --fungus
mv genemark.gtf $DATADIR/annotation/JL221
mv gmhmm.mod $DATADIR/annotation/JL221
mv run.cfg $DATADIR/annotation/JL221
funannotate predict -i $DATADIR/assembly/JL221/scaffolds.masked.fasta \
-o $DATADIR/annotation/JL221 \
-s "Microbotryomycetes sp" --strain JL221 \
--protein_evidence $DATADIR/annotation/Rhoto1_GeneCatalog_proteins_20141208.aa.fasta \
--busco_db basidiomycota \
--genemark_gtf $DATADIR/annotation/JL221/genemark.gtf \
--cpus 16
conda deactivate
scontrol show job $SLURM_JOB_ID ### write job information to output file