Alternate assembly has better scaffold N50 stats than primary assembly

[afiyachida]

Hi,
I am trying to assemble a butterfly genome. The scaffolded assembly has better stats in the alternate haplotype when compared to the primary.
I am not sure why this could be happening. Is there any parameter that I need to alter?

The current command that I am using is :

yahs \ -o Butterfly_209_full.purged.asm.bp.hap1.p_ctg.cleaned_sequences.fa.cleaned.fasta.purged \ unzipped.fasta \ hic_R1R2.bam \ -l 10 --no-contig-ec -e GATC,GANTC,CTNAG,TTAA

The log files for primary and alternate assembly are given below:

Primary:

[I::find_re_from_seqs] number restriction enzyme cutting sites found in sequences: 35041702
[I::find_re_from_seqs] restriction enzyme cutting sites density: 0.034889
[I::main] dump hic links (BAM) to binary file Butterfly_209_full.purged.asm.bp.hap1.p_ctg.cleaned_sequences.fa.cleaned.fasta.purged.bin
[I::dump_links_from_bam_file] 1 million records processed, 458645 read pairs
[I::dump_links_from_bam_file] 2 million records processed, 916588 read pairs
[I::dump_links_from_bam_file] 3 million records processed, 1374251 read pairs
[I::dump_links_from_bam_file] 4 million records processed, 1831434 read pairs
[I::dump_links_from_bam_file] 5 million records processed, 2288230 read pairs
[I::dump_links_from_bam_file] 6 million records processed, 2744830 read pairs
[I::dump_links_from_bam_file] 7 million records processed, 3200668 read pairs
[I::dump_links_from_bam_file] 8 million records processed, 3656636 read pairs
[I::dump_links_from_bam_file] 9 million records processed, 4112349 read pairs
[I::dump_links_from_bam_file] 10 million records processed, 4567723 read pairs
[I::dump_links_from_bam_file] 11 million records processed, 5022960 read pairs
[I::dump_links_from_bam_file] 12 million records processed, 5478133 read pairs
[I::dump_links_from_bam_file] 13 million records processed, 5932625 read pairs
[I::dump_links_from_bam_file] 14 million records processed, 6386917 read pairs
[I::dump_links_from_bam_file] 15 million records processed, 6840882 read pairs
[I::dump_links_from_bam_file] 16 million records processed, 7294514 read pairs
[I::dump_links_from_bam_file] 17 million records processed, 7747994 read pairs
[I::dump_links_from_bam_file] 18 million records processed, 8201116 read pairs
[I::dump_links_from_bam_file] 19 million records processed, 8653687 read pairs
[I::dump_links_from_bam_file] 20 million records processed, 9106097 read pairs
[I::dump_links_from_bam_file] 21 million records processed, 9558279 read pairs
[I::dump_links_from_bam_file] 22 million records processed, 10009966 read pairs
[I::dump_links_from_bam_file] 23 million records processed, 10461192 read pairs
[I::dump_links_from_bam_file] 24 million records processed, 10912246 read pairs
[I::dump_links_from_bam_file] 25 million records processed, 11363010 read pairs
[I::dump_links_from_bam_file] dumped 11672306 read pairs from 25686181 records: 7313270 intra links + 4359036 inter links
[I::run_yahs] RAM total: 1511.530GB
[I::run_yahs] RAM limit: 4.546GB
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 920373 (n = 309)
[I::print_asm_stats] N90: 222262 (n = 1145)
[I::print_asm_stats] N100: 4181 (n = 2265)
[I::run_yahs] scaffolding round 1 resolution = 10000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 2810.497 6497301.000 0.000
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 1 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 1426182 (n = 209)
[I::print_asm_stats] N90: 332509 (n = 762)
[I::run_yahs] scaffolding round 2 resolution = 20000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 2433.188 5010115.000 0.000
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 2 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 1806670 (n = 163)
[I::print_asm_stats] N90: 451263 (n = 575)
[I::run_yahs] scaffolding round 3 resolution = 50000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.001
[I::inter_link_norms] average link count: 12406.761 10937690.000 0.001
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 3 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 2608756 (n = 116)
[I::print_asm_stats] N90: 578032 (n = 414)
[I::run_yahs] scaffolding round 4 resolution = 100000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.013
[I::inter_link_norms] average link count: 25339.713 7499407.000 0.003
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 4 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 3505773 (n = 88)
[I::print_asm_stats] N90: 728842 (n = 314)
[I::run_yahs] scaffolding round 5 resolution = 200000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.101
[I::inter_link_norms] average link count: 18477.101 2607631.000 0.007
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 5 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 4930469 (n = 61)
[I::print_asm_stats] N90: 836633 (n = 230)
[I::run_yahs] scaffolding round 6 resolution = 500000
[I::run_yahs] assembly N50 (4930469) too small. End of scaffolding.
[I::main] writing FASTA file for scaffolds
[I::write_fasta_file_from_agp] Number sequences: 863
[I::write_fasta_file_from_agp] Number bases: 1004649243
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 4930469 (n = 61)
[I::print_asm_stats] N90: 836633 (n = 230)
[I::print_asm_stats] N100: 4181 (n = 863)
[I::main] Version: 1.2a.1

Alternate:

[I::find_re_from_seqs] number restriction enzyme cutting sites found in sequences: 54317138
[I::find_re_from_seqs] restriction enzyme cutting sites density: 0.034858
[I::main] dump hic links (BAM) to binary file Butterfly_209_alternate_contigs_full.purged.bin
[I::dump_links_from_bam_file] 1 million records processed, 467037 read pairs
[I::dump_links_from_bam_file] 2 million records processed, 933057 read pairs
[I::dump_links_from_bam_file] 3 million records processed, 1399320 read pairs
[I::dump_links_from_bam_file] 4 million records processed, 1865490 read pairs
[I::dump_links_from_bam_file] 5 million records processed, 2331075 read pairs
[I::dump_links_from_bam_file] 6 million records processed, 2796521 read pairs
[I::dump_links_from_bam_file] 7 million records processed, 3261481 read pairs
[I::dump_links_from_bam_file] 8 million records processed, 3725991 read pairs
[I::dump_links_from_bam_file] 9 million records processed, 4190027 read pairs
[I::dump_links_from_bam_file] 10 million records processed, 4654282 read pairs
[I::dump_links_from_bam_file] 11 million records processed, 5118441 read pairs
[I::dump_links_from_bam_file] 12 million records processed, 5582360 read pairs
[I::dump_links_from_bam_file] 13 million records processed, 6045748 read pairs
[I::dump_links_from_bam_file] 14 million records processed, 6509276 read pairs
[I::dump_links_from_bam_file] 15 million records processed, 6972591 read pairs
[I::dump_links_from_bam_file] 16 million records processed, 7435824 read pairs
[I::dump_links_from_bam_file] 17 million records processed, 7898732 read pairs
[I::dump_links_from_bam_file] 18 million records processed, 8361401 read pairs
[I::dump_links_from_bam_file] 19 million records processed, 8823528 read pairs
[I::dump_links_from_bam_file] 20 million records processed, 9285682 read pairs
[I::dump_links_from_bam_file] 21 million records processed, 9747431 read pairs
[I::dump_links_from_bam_file] 22 million records processed, 10209188 read pairs
[I::dump_links_from_bam_file] 23 million records processed, 10670742 read pairs
[I::dump_links_from_bam_file] 24 million records processed, 11131857 read pairs
[I::dump_links_from_bam_file] 25 million records processed, 11593003 read pairs
[I::dump_links_from_bam_file] 26 million records processed, 12053568 read pairs
[I::dump_links_from_bam_file] 27 million records processed, 12513720 read pairs
[I::dump_links_from_bam_file] 28 million records processed, 12973497 read pairs
[I::dump_links_from_bam_file] 29 million records processed, 13432829 read pairs
[I::dump_links_from_bam_file] 30 million records processed, 13892255 read pairs
[I::dump_links_from_bam_file] 31 million records processed, 14351765 read pairs
[I::dump_links_from_bam_file] 32 million records processed, 14811129 read pairs
[I::dump_links_from_bam_file] 33 million records processed, 15269883 read pairs
[I::dump_links_from_bam_file] dumped 15594174 read pairs from 33706620 records: 9815185 intra links + 5778989 inter links
[I::run_yahs] RAM total: 1511.530GB
[I::run_yahs] RAM limit: 2.878GB
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 1323643 (n = 359)
[I::print_asm_stats] N90: 389480 (n = 1195)
[I::print_asm_stats] N100: 5164 (n = 2094)
[I::run_yahs] scaffolding round 1 resolution = 10000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 2077.359 6266679.000 0.000
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 1 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 1883528 (n = 246)
[I::print_asm_stats] N90: 546048 (n = 827)
[I::run_yahs] scaffolding round 2 resolution = 20000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 2093.374 5775616.000 0.000
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 2 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 1323643 (n = 359)
[I::print_asm_stats] N90: 389480 (n = 1195)
[I::print_asm_stats] N100: 5164 (n = 2094)
[I::run_yahs] scaffolding round 1 resolution = 10000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 2077.359 6266679.000 0.000
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 1 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 1883528 (n = 246)
[I::print_asm_stats] N90: 546048 (n = 827)
[I::run_yahs] scaffolding round 2 resolution = 20000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 2093.374 5775616.000 0.000
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 2 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 2674667 (n = 169)
[I::print_asm_stats] N90: 681846 (n = 613)
[I::run_yahs] scaffolding round 3 resolution = 50000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.000
[I::inter_link_norms] average link count: 6460.794 8791646.000 0.001
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 3 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 3695363 (n = 129)
[I::print_asm_stats] N90: 934477 (n = 439)
[I::run_yahs] scaffolding round 4 resolution = 100000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.002
[I::inter_link_norms] average link count: 23243.655 9429500.000 0.002
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 4 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 4998835 (n = 96)
[I::print_asm_stats] N90: 1178019 (n = 325)
[I::run_yahs] scaffolding round 5 resolution = 200000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.033
[I::inter_link_norms] average link count: 32293.811 4730835.000 0.007
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 5 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 6868390 (n = 75)
[I::print_asm_stats] N90: 1478584 (n = 249)
[I::run_yahs] scaffolding round 6 resolution = 500000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 0.370
[I::inter_link_norms] average link count: 19300.748 981169.000 0.020
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 6 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 10684921 (n = 45)
[I::print_asm_stats] N90: 1533950 (n = 182)
[I::run_yahs] scaffolding round 7 resolution = 1000000
[I::run_scaffolding] starting norm estimation...
[I::run_scaffolding] starting link estimation...
[I::inter_link_norms] using noise level 1.609
[I::inter_link_norms] average link count: 4940.189 215854.000 0.023
[I::run_scaffolding] starting scaffolding graph contruction...
[I::run_yahs] scaffolding round 7 done
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 16227411 (n = 28)
[I::print_asm_stats] N90: 1515747 (n = 139)
[I::run_yahs] scaffolding round 8 resolution = 2000000
[I::run_yahs] assembly N50 (16227411) too small. End of scaffolding.
[I::main] writing FASTA file for scaffolds
[I::write_fasta_file_from_agp] Number sequences: 584
[I::write_fasta_file_from_agp] Number bases: 1558545293
[I::print_asm_stats] assembly stats:
[I::print_asm_stats] N50: 16227411 (n = 28)
[I::print_asm_stats] N90: 1515747 (n = 139)
[I::print_asm_stats] N100: 5164 (n = 584)
[I::main] Version: 1.2a.1

Any help would be appreciated to resolve this. Thank you!