15-CRAQ_Final.sh

#$ -N CRAQ
#$ -o ../../logs/$JOB_NAME.$JOB_ID.log
#$ -e ../../logs/$JOB_NAME.$JOB_ID.err
#$ -cwd
#$ -P Test.p
#$ -pe smp 240
#$ -l h_vmem=4.1g
#$ -t 1:3
#$ -tc 3

#############################################################
GENOME_DIR=/mnt/data/arslan/Teas/01_Assembly/scaffolding

conda activate /mnt/bin/craq/env
export PATH=/mnt/bin/craq/CRAQ/bin/:$PATH

craq -t $NSLOTS -pl T \
-g ${GENOME_DIR}/${SEED}-scaffold/${SEED}_rename.scaffold.fasta \
-sms ../output_carq/${SEED}.sort.bam \
-D ../output_carq/${SEED}.carq.out