/usr/local/SALSA/break_contigs_start -a SALSA_HiC/alignment_iteration_1.bed -l SALSA_HiC/scaffold_length_iteration_1 -s 100 > SALSA_HiC/input_breakspython2 /usr/local/SALSA/correct.py  input_2/hatahifihic.hic.p_ctg.gfa.fa SALSA_HiC/input_breaks SALSA_HiC/alignment_iteration_1.bed SALSA_HiCpython2 /usr/local/SALSA/RE_sites.py -a SALSA_HiC/assembly.cleaned.fasta -e DNASE > SALSA_HiC/re_counts_iteration_1
python2 /usr/local/SALSA/make_links.py -b SALSA_HiC/alignment_iteration_1.bed -d SALSA_HiC -i 1 -x abc
python2 /usr/local/SALSA/fast_scaled_scores.py -d SALSA_HiC -i 1
sort -k 5 -gr SALSA_HiC/contig_links_scaled_iteration_1 > SALSA_HiC/contig_links_scaled_sorted_iteration_1
python2 /usr/local/SALSA/layout_unitigs.py -x abc -l SALSA_HiC/contig_links_scaled_sorted_iteration_1 -c 1000 -i 1 -d SALSA_HiC
/usr/local/SALSA/break_contigs -a SALSA_HiC/alignment_iteration_2.bed -b SALSA_HiC/breakpoints_iteration_2.txt -l SALSA_HiC/scaffold_length_iteration_2 -i 2 -s 100   > SALSA_HiC/misasm_iteration_2.report
python2 /usr/local/SALSA/refactor_breaks.py -d SALSA_HiC -i 2
python2 /usr/local/SALSA/make_links.py -b SALSA_HiC/alignment_iteration_2.bed -d SALSA_HiC -i 2
python2 /usr/local/SALSA/fast_scaled_scores.py -d SALSA_HiC -i 2
sort -k 5 -gr SALSA_HiC/contig_links_scaled_iteration_2 > SALSA_HiC/contig_links_scaled_sorted_iteration_2
python2 /usr/local/SALSA/layout_unitigs.py -x abc -l SALSA_HiC/contig_links_scaled_sorted_iteration_2 -c 1000 -i 2 -d SALSA_HiC
/usr/local/SALSA/break_contigs -a SALSA_HiC/alignment_iteration_3.bed -b SALSA_HiC/breakpoints_iteration_3.txt -l SALSA_HiC/scaffold_length_iteration_3 -i 3 -s 100  > SALSA_HiC/misasm_iteration_3.report
python2 /usr/local/SALSA/refactor_breaks.py -d SALSA_HiC -i 3 > SALSA_HiC/misasm_3.log
python2 /usr/local/SALSA/make_links.py -b SALSA_HiC/alignment_iteration_3.bed -d SALSA_HiC -i 3
python2 /usr/local/SALSA/fast_scaled_scores.py -d SALSA_HiC -i 3
sort -k 5 -gr SALSA_HiC/contig_links_scaled_iteration_3 > SALSA_HiC/contig_links_scaled_sorted_iteration_3
python2 /usr/local/SALSA/layout_unitigs.py -x abc -l SALSA_HiC/contig_links_scaled_sorted_iteration_3 -c 1000 -i 3 -d SALSA_HiC
/usr/local/SALSA/break_contigs -a SALSA_HiC/alignment_iteration_4.bed -b SALSA_HiC/breakpoints_iteration_4.txt -l SALSA_HiC/scaffold_length_iteration_4 -i 4 -s 100  > SALSA_HiC/misasm_iteration_4.report
python2 /usr/local/SALSA/refactor_breaks.py -d SALSA_HiC -i 4 > SALSA_HiC/misasm_4.log
python2 /usr/local/SALSA/make_links.py -b SALSA_HiC/alignment_iteration_4.bed -d SALSA_HiC -i 4
python2 /usr/local/SALSA/fast_scaled_scores.py -d SALSA_HiC -i 4
sort -k 5 -gr SALSA_HiC/contig_links_scaled_iteration_4 > SALSA_HiC/contig_links_scaled_sorted_iteration_4
python2 /usr/local/SALSA/layout_unitigs.py -x abc -l SALSA_HiC/contig_links_scaled_sorted_iteration_4 -c 1000 -i 4 -d SALSA_HiC
/usr/local/SALSA/break_contigs -a SALSA_HiC/alignment_iteration_5.bed -b SALSA_HiC/breakpoints_iteration_5.txt -l SALSA_HiC/scaffold_length_iteration_5 -i 5 -s 100  > SALSA_HiC/misasm_iteration_5.report
python2 /usr/local/SALSA/refactor_breaks.py -d SALSA_HiC -i 5 > SALSA_HiC/misasm_5.log
python2 /usr/local/SALSA/get_seq.py -a SALSA_HiC/assembly.cleaned.fasta -f SALSA_HiC/scaffolds_FINAL.fasta -g SALSA_HiC/scaffolds_FINAL.agp -p SALSA_HiC/scaffolds_iteration_3.p