#!/bin/bash #SBATCH --job-name=Pig #SBATCH --output=Pig.out #SBATCH --error=Pig.err #SBATCH --partition=GPU-2080 #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=28 #SBATCH --mem=50G
Work_Dir="/home/students/q.abbas/pig" genome="/home/students/q.abbas/pig/" proteindb="/proj/q.abbas/databases/Proteomics/metazoa/OrthoDB_Metazoa.fa" Species="pig" mkdir -p $Work_Dir/braker mkdir -p $Work_Dir/braker/default mkdir -p $Work_Dir/braker/seeds mkdir -p $Work_Dir/braker/prothint mkdir -p $Work_Dir/braker/relaxed rm -rf /home/students/q.abbas/Tools/Augustus/config/species/pig
echo "start default of
/home/students/q.abbas/Tools/BRAKER-2.1.6/scripts/braker.pl
--species=$Species --softmasking --cores 48
--workingdir=$Work_Dir/braker/default/
--genome=$genome
--prot_seq=$proteindb
&& echo "Default Finished*****"
/home/students/q.abbas/Tools/BRAKER-2.1.6/scripts/braker.pl
--species=pig --softmasking --skipAllTraining --cores 48
--workingdir=$Work_Dir/braker/seeds/
--genome=$genome
--hints=$Work_Dir/braker/default/hintsfile.gff
&& echo "Generative $folder Finished*****"
/home/students/q.abbas/Tools/ProtHint-2.6.0/bin/prothint.py
--threads=48 --workdir $Work_Dir/braker/default/prothint/ $genome $proteindb
--geneSeeds=$Work_Dir/braker/default/seeds/augustus.hints.gtf \ && grep -v src=M $Work_Dir/braker/default/prothint/prothint_augustus.gff | grep -v src=C
> $Work_Dir/braker/default/prothint/evidence_no_M_C.gff
&& echo "Prothint $folder Finished*****"
/home/students/q.abbas/Tools/BRAKER-2.1.6/scripts/braker.pl
--skipAllTraining --species=pig --cores 48
--hints $Work_Dir/braker/default/prothint/evidence_no_M_C.gff \ --genome=$genome
--workingdir=$Work_Dir/braker/default/relaxed/
--augustus_args "--minexonintronprob=0 --minmeanexonintronprob=0
--maxtracks=20 --sample=1000 --alternatives-from-sampling=true --temperature=3"
--extrinsicCfgFiles /home/students/q.abbas/Tools/BRAKER-2.1.6/scripts/cfg/ep_smallMalus.cfg
&& echo "Relaxed $folder Finished*****"