Number of iterations is always 3, even with -i flag

[shouryaj]

Hi,

The number of iterations SALSA runs is always 3, even though I pass it the -i flag with different number of iterations. The exact command I ran and the output is below:

sudo python run_pipeline.py -a /home/shourj/mylerlab/canu.contigs.chromosomes.fasta -l /home/shourj/mylerlab/canu.contigs.chromosomes.fasta.fai -b /home/shourj/mylerlab/canu_arima.bed -e GATC -o scaffoldTEST -i 35 -m yes
bedfile loaded
python /home/shourj/SALSA/RE_sites.py -a scaffoldTEST/assembly.cleaned.fasta -e GATC > scaffoldTEST/re_counts_itera
tion_1
Starting Iteration 1
python /home/shourj/SALSA/make_links.py -b scaffoldTEST/alignment_iteration_1.bed -d scaffoldTEST -i 1 -x abc
bedfile started
bedfile loaded
python /home/shourj/SALSA/fast_scaled_scores.py -d scaffoldTEST -i 1
sort -k 5 -gr scaffoldTEST/contig_links_scaled_iteration_1 > scaffoldTEST/contig_links_scaled_sorted_iteration_1
python /home/shourj/SALSA/layout_unitigs.py -x abc -u abc -t abc -l scaffoldTEST/contig_links_scaled_sorted_iterati
on_1 -c 1000 -i 1 -d scaffoldTEST
Loading Hi-C links
Finished loading Hi-C links, Loading unitig links now..
Hybrid scaffold graph loaded, nodes = 134 edges = 105
Hi-C implied edges = 0
Unitig tiling implied edges = 0
Assembly graph implied edges = 0
10x implied edges = 0
/home/shourj/SALSA/break_contigs -a scaffoldTEST/alignment_iteration_2.bed -b scaffoldTEST/breakpoints_iteration_2.
txt -l scaffoldTEST/scaffold_length_iteration_2 -i 2 > scaffoldTEST/misasm_iteration_2.report
python /home/shourj/SALSA/refactor_breaks.py -d scaffoldTEST -i 2
Starting Iteration 2
python /home/shourj/SALSA/make_links.py -b scaffoldTEST/alignment_iteration_2.bed -d scaffoldTEST -i 2
bedfile started
bedfile loaded
Starting Iteration 2
python /home/shourj/SALSA/layout_unitigs.py -x abc -u abc -t abc -l scaffoldTEST/contig_links_scaled_sorted_iterati
on_2 -c 1000 -i 2 -d scaffoldTEST
Loading Hi-C links
Finished loading Hi-C links, Loading unitig links now..
Hybrid scaffold graph loaded, nodes = 36 edges = 27
Hi-C implied edges = 0
Unitig tiling implied edges = 0
Assembly graph implied edges = 0
10x implied edges = 0
/home/shourj/SALSA/break_contigs -a scaffoldTEST/alignment_iteration_3.bed -b scaffoldTEST/breakpoints_iteration_3.
txt -l scaffoldTEST/scaffold_length_iteration_3 -i 3 > scaffoldTEST/misasm_iteration_3.report
python /home/shourj/SALSA/refactor_breaks.py -d scaffoldTEST -i 3 > scaffoldTEST/misasm_3.log
Starting Iteration 3
python /home/shourj/SALSA/make_links.py -b scaffoldTEST/alignment_iteration_3.bed -d scaffoldTEST -i 3
bedfile started
bedfile loaded
Starting Iteration 3
python /home/shourj/SALSA/layout_unitigs.py -x abc -u abc -t abc -l scaffoldTEST/contig_links_scaled_sorted_iterati
on_3 -c 1000 -i 3 -d scaffoldTEST
Loading Hi-C links
Finished loading Hi-C links, Loading unitig links now..
Hybrid scaffold graph loaded, nodes = 16 edges = 11
Hi-C implied edges = 0
Unitig tiling implied edges = 0
Assembly graph implied edges = 0
10x implied edges = 0
/home/shourj/SALSA/break_contigs -a scaffoldTEST/alignment_iteration_4.bed -b scaffoldTEST/breakpoints_iteration_4.
txt -l scaffoldTEST/scaffold_length_iteration_4 -i 4 > scaffoldTEST/misasm_iteration_4.report
python /home/shourj/SALSA/refactor_breaks.py -d scaffoldTEST -i 4 > scaffoldTEST/misasm_4.log

Am i just running the command wrong?

Thanks!

[ghuryejay]

Hi,

Can you share the list of the output files generated in the scaffoldTEST folder? Also, can you provide the output of tail -n 4 misasm_iteration_3.report and tail -n 4 misasm_iteration_4.report?

[shouryaj]

Sure. The list of files is:

alignment_iteration_1.bed contig_links_scaled_sorted_iteration_1 re_counts_iteration_1
alignment_iteration_2.bed contig_links_scaled_sorted_iteration_2 re_counts_iteration_2
alignment_iteration_3.bed contig_links_scaled_sorted_iteration_3 re_counts_iteration_3
alignment_iteration_4.bed input_breaks re_counts_iteration_4
assembly.cleaned.fasta links_avoid_iteration_2 scaffold_length_iteration_1
breakpoints_iteration_2.txt links_avoid_iteration_3 scaffold_length_iteration_2
breakpoints_iteration_3.txt links_avoid_iteration_4 scaffold_length_iteration_3
breakpoints_iteration_4.txt misasm_2.DONE scaffold_length_iteration_4
commands.log misasm_3.DONE scaffolds_FINAL.agp
contig_links_iteration_1 misasm_3.log scaffolds_FINAL.fasta
contig_links_iteration_2 misasm_4.DONE scaffolds_iteration_1.p
contig_links_iteration_3 misasm_4.log scaffolds_iteration_2.p
contig_links_scaled_iteration_1 misasm_iteration_2.report scaffolds_iteration_3.p
contig_links_scaled_iteration_2 misasm_iteration_3.report
contig_links_scaled_iteration_3 misasm_iteration_4.report

"tail -n 4 misasm_iteration_3.report" result:
scaffold_6
Total Joins = 1
Suspicious Joins = 0
Percent Suspicious Joins = 0

"tail -n 4 misasm_iteration_4.report" result:
scaffold_1
Total Joins = 0
Suspicious Joins = 0
Percent Suspicious Joins = -nan

[ghuryejay]

Okay. This means that SALSA stopped scaffolding after 3rd iteration because there are no Hi-C links to scaffold. If your Hi-C data is high coverage, the scaffolding would run for more iterations.

…

On Fri, Mar 30, 2018 at 2:08 PM, shouryaj ***@***.***> wrote: Sure. The list of files is: alignment_iteration_1.bed contig_links_scaled_sorted_iteration_1 re_counts_iteration_1 alignment_iteration_2.bed contig_links_scaled_sorted_iteration_2 re_counts_iteration_2 alignment_iteration_3.bed contig_links_scaled_sorted_iteration_3 re_counts_iteration_3 alignment_iteration_4.bed input_breaks re_counts_iteration_4 assembly.cleaned.fasta links_avoid_iteration_2 scaffold_length_iteration_1 breakpoints_iteration_2.txt links_avoid_iteration_3 scaffold_length_iteration_2 breakpoints_iteration_3.txt links_avoid_iteration_4 scaffold_length_iteration_3 breakpoints_iteration_4.txt misasm_2.DONE scaffold_length_iteration_4 commands.log misasm_3.DONE scaffolds_FINAL.agp contig_links_iteration_1 misasm_3.log scaffolds_FINAL.fasta contig_links_iteration_2 misasm_4.DONE scaffolds_iteration_1.p contig_links_iteration_3 misasm_4.log scaffolds_iteration_2.p contig_links_scaled_iteration_1 misasm_iteration_2.report scaffolds_iteration_3.p contig_links_scaled_iteration_2 misasm_iteration_3.report contig_links_scaled_iteration_3 misasm_iteration_4.report "tail -n 4 misasm_iteration_3.report" result: scaffold_6 Total Joins = 1 Suspicious Joins = 0 Percent Suspicious Joins = 0 "tail -n 4 misasm_iteration_4.report" result: scaffold_1 Total Joins = 0 Suspicious Joins = 0 Percent Suspicious Joins = -nan — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA8OKCQM_1m1UYDOWfNO4-Tm8EZ-0mwVks5tjnSZgaJpZM4TBR9r> .

-- Best, Jay