echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 1  --readFile -o 1.hon " | msub -N 'hon1'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 2  --readFile -o 2.hon " | msub -N 'hon2'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 3  --readFile -o 3.hon " | msub -N 'hon3'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 4  --readFile -o 4.hon " | msub -N 'hon4'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 5  --readFile -o 5.hon " | msub -N 'hon5'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 6  --readFile -o 6.hon " | msub -N 'hon6'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 7  --readFile -o 7.hon " | msub -N 'hon7'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 8  --readFile -o 8.hon " | msub -N 'hon8'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 9  --readFile -o 9.hon " | msub -N 'hon9'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 10 --readFile -o 10.hon" | msub -N 'hon10' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 11 --readFile -o 11.hon" | msub -N 'hon11' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 12 --readFile -o 12.hon" | msub -N 'hon12' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 13 --readFile -o 13.hon" | msub -N 'hon13' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 14 --readFile -o 14.hon" | msub -N 'hon14' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 15 --readFile -o 15.hon" | msub -N 'hon15' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 16 --readFile -o 16.hon" | msub -N 'hon16' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 17 --readFile -o 17.hon" | msub -N 'hon17' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 18 --readFile -o 18.hon" | msub -N 'hon18' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 19 --readFile -o 19.hon" | msub -N 'hon19' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 20 --readFile -o 20.hon" | msub -N 'hon20' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 21 --readFile -o 21.hon" | msub -N 'hon21' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom 22 --readFile -o 22.hon" | msub -N 'hon22' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom MT --readFile -o MT.hon" | msub -N 'honMT' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
echo "Honey.py spots CHM1.bam --nproc 8 -b 25 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom X  --readFile -o X.hon " | msub -N 'honX'  -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
#echo "Honey.py spots CHM1.bam --nproc 8 -e 3 -E 5 --reference ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta --chrom Y  --readFile -o Y.hon " | msub -N 'honY' -q three_hours -d `pwd`/ -l nodes=1:ppn=4,mem=48000mb -A prog-ng0004
