iterations stop after 8

[gf777]

Hi,

I have run into an issue while trying to run many iterations of salsa to scaffold a targeted set of smaller unplaced scaffolds. Here is how I run it:

python $tools/salsa2/SALSA-2.2/run_pipeline.py -a $1 -l $2 -e ${enz} -b $3 -o $4 -m yes -p yes -i $5 -s $6

With -i above 8, no matter ho bigger than that, it stops at 8 iterations. -s is set to 20,000,000 (without commas), about the size of what I want to assemble. I also noticed that is with -s I use a very low value, say 500000 or very high 500,000,000, it stops after the canonical 3 rounds no matter what the value of -i is.

Here is an example of the log:

bedfile loaded
Starting Iteration 1
bedfile started
bedfile loaded
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 246 edges = 151
Hi-C implied edges = 0
Starting Iteration 2
bedfile started
bedfile loaded
Starting Iteration 2
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 230 edges = 123
Hi-C implied edges = 0
Starting Iteration 3
bedfile started
bedfile loaded
Starting Iteration 3
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 172 edges = 89
Hi-C implied edges = 0
Starting Iteration 4
bedfile started
bedfile loaded
Starting Iteration 4
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 190 edges = 101
Hi-C implied edges = 0
Starting Iteration 5
bedfile started
bedfile loaded
Starting Iteration 5
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 188 edges = 98
Hi-C implied edges = 0
Starting Iteration 6
bedfile started
bedfile loaded
Starting Iteration 6
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 202 edges = 103
Hi-C implied edges = 0
Starting Iteration 7
bedfile started
bedfile loaded
Starting Iteration 7
Loading Hi-C links
Hybrid scaffold graph loaded, nodes = 228 edges = 116
Hi-C implied edges = 0
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/RE_sites.py -a test4/assembly.cleaned.fasta -e GATC,GANTC > test4/re_counts_iteration_1
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_1.bed -d test4 -i 1 -x abc
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/fast_scaled_scores.py -d test4 -i 1
sort -k 5 -gr test4/contig_links_scaled_iteration_1 > test4/contig_links_scaled_sorted_iteration_1
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_1 -c 1000 -i 1 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_2.bed -b test4/breakpoints_iteration_2.txt -l test4/scaffold_length_iteration_2 -i 2 -s 100 > test4/misasm_iteration_2.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 2
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_2.bed -d test4 -i 2
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_2 -c 1000 -i 2 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_3.bed -b test4/breakpoints_iteration_3.txt -l test4/scaffold_length_iteration_3 -i 3 -s 100 > test4/misasm_iteration_3.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 3 > test4/misasm_3.log
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_3.bed -d test4 -i 3
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_3 -c 1000 -i 3 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_4.bed -b test4/breakpoints_iteration_4.txt -l test4/scaffold_length_iteration_4 -i 4 -s 100 > test4/misasm_iteration_4.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 4 > test4/misasm_4.log
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_4.bed -d test4 -i 4
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_4 -c 1000 -i 4 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_5.bed -b test4/breakpoints_iteration_5.txt -l test4/scaffold_length_iteration_5 -i 5 -s 100 > test4/misasm_iteration_5.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 5 > test4/misasm_5.log
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_5.bed -d test4 -i 5
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_5 -c 1000 -i 5 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_6.bed -b test4/breakpoints_iteration_6.txt -l test4/scaffold_length_iteration_6 -i 6 -s 100 > test4/misasm_iteration_6.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 6 > test4/misasm_6.log
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_6.bed -d test4 -i 6
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_6 -c 1000 -i 6 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_7.bed -b test4/breakpoints_iteration_7.txt -l test4/scaffold_length_iteration_7 -i 7 -s 100 > test4/misasm_iteration_7.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 7 > test4/misasm_7.log
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/make_links.py -b test4/alignment_iteration_7.bed -d test4 -i 7
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/layout_unitigs.py -x abc -l test4/contig_links_scaled_sorted_iteration_7 -c 1000 -i 7 -d test4
/rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/break_contigs -a test4/alignment_iteration_8.bed -b test4/breakpoints_iteration_8.txt -l test4/scaffold_length_iteration_8 -i 8 -s 100 > test4/misasm_iteration_8.report
python /rugpfs/fs0/vgl/store/vglshare/tools/VGP-tools/salsa2/SALSA-2.2/refactor_breaks.py -d test4 -i 8 > test4/misasm_8.log

Any suggestion on how could I run this well above 8 times in the same cycle, and reasons for not to do so?

Many thanks

Giulio