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#!/bin/shbash

#$ -N modeler
#$ -pe *mpisingle 20
#$ -cwd

module load bioinfo/RepeatTools/repeat_env

#Prije pokretanja potrebno je kreirati bazu
BuildDatabase -name elephant GCF_000001905.1_Loxafr3.0_genomic.fna

RepeatModeler -database elephant -threads $NSLOTS -LTRStruct >& run.out

#!/bin/shbash

#$ -N masker
#$ -pe *mpisingle 20
#$ -cwd

module load bioinfo/RepeatTools/repeat_env

RepeatMasker --species Loxodonta_africana GCF_000001905.1_Loxafr3.0_genomic.fna -pa $NSLOTS

#!/bin/shbash

#$ -N explorer
#$ -pe *mpisingle 20
#$ -cwd
#$ -l memory=2

module load bioinfo/RepeatTools/repeat_env

seqclust -c $NSLOTS -r 41943040 GCF_000001905.1_Loxafr3.0_genomic.fna