ALLHiC used for Pacbio hifi data (assembled by hifiasm)

[xiaobaiymq]

Hello I use hifiasm to assemble the Pacbio hifi data, and then use allhic to anchor the obtained haplotypes to the chromosomes. my genome is diploid, and 9 chromosomes (2x=2n=18). When I use K=9 and 10, one scaffold is very long（close to 200M，but my genome is just 300M). Now, I don't know how to do.

My command： ALLHiC_partition -b $prunning_bam -r $draft -e GATC -k 10 && ALLHiC_rescue -b $clean_bam -r $draft
-c prunning.clusters.txt
-i prunning.counts_GATC.txt &&

allhic extract $clean_bam $draft --RE GATC && for i in group*.txt; do allhic optimize $i nfmj_hap1_clean.clm done &&

ALLHiC_build $draft &&

samtools faidx groups.asm.fasta && cut -f 1,2 groups.asm.fasta.fai > chrn.list && ALLHiC_plot $clean_bam groups.agp chrn.list 500k pdf

chrn.list group1 205476565 group10 455973 group2 34444728 group3 31642448 group4 28043948 group5 21055410 group6 10873773 group7 8727916 group8 3688058 group9 620793 h1tg000256l 25749 500K_all_chrs.pdf