How to correctly reassignment？

[zjygoo]

Hello, Xiaofei. I'm having some small issues with HapHiC. My species is an autotetraploid (2n=4x=44), and I used p_utg generated by hifiasm as the input file. When clustering, the command is as follows: haphic cluster genome.final.fasta HiC.filtered.bam 44 --threads 80 The result is as follows: 2024-04-29 09:48:41 <HapHiC_cluster.py> [recommend_inflation] You could try inflation from 1.5 (length ratio = 0.75) Entering the recommended inflation factor 1.5 folder: -rw-rw-r-- 1 ps ps 152 4月 29 09:48 group10_32091997bp.txt -rw-rw-r-- 1 ps ps 368 4月 29 09:48 group11_31248394bp.txt -rw-rw-r-- 1 ps ps 153 4月 29 09:48 group12_29837997bp.txt -rw-rw-r-- 1 ps ps 215 4月 29 09:48 group13_29756760bp.txt -rw-rw-r-- 1 ps ps 185 4月 29 09:48 group1_41105304bp.txt -rw-rw-r-- 1 ps ps 214 4月 29 09:48 group14_29336476bp.txt -rw-rw-r-- 1 ps ps 119 4月 29 09:48 group15_27944639bp.txt -rw-rw-r-- 1 ps ps 89 4月 29 09:48 group16_26507170bp.txt -rw-rw-r-- 1 ps ps 182 4月 29 09:48 group17_26402146bp.txt -rw-rw-r-- 1 ps ps 243 4月 29 09:48 group18_26392657bp.txt -rw-rw-r-- 1 ps ps 151 4月 29 09:48 group19_26370085bp.txt -rw-rw-r-- 1 ps ps 308 4月 29 09:48 group20_26103341bp.txt -rw-rw-r-- 1 ps ps 213 4月 29 09:48 group21_25795553bp.txt -rw-rw-r-- 1 ps ps 152 4月 29 09:48 group22_23983702bp.txt -rw-rw-r-- 1 ps ps 119 4月 29 09:48 group23_23911665bp.txt -rw-rw-r-- 1 ps ps 184 4月 29 09:48 group2_39247364bp.txt -rw-rw-r-- 1 ps ps 121 4月 29 09:48 group24_23558558bp.txt -rw-rw-r-- 1 ps ps 150 4月 29 09:48 group25_23164941bp.txt -rw-rw-r-- 1 ps ps 208 4月 29 09:48 group26_22711677bp.txt -rw-rw-r-- 1 ps ps 151 4月 29 09:48 group27_22662324bp.txt -rw-rw-r-- 1 ps ps 244 4月 29 09:48 group28_22502537bp.txt -rw-rw-r-- 1 ps ps 120 4月 29 09:48 group29_21592425bp.txt -rw-rw-r-- 1 ps ps 211 4月 29 09:48 group30_19931306bp.txt -rw-rw-r-- 1 ps ps 151 4月 29 09:48 group31_18740276bp.txt -rw-rw-r-- 1 ps ps 119 4月 29 09:48 group32_18509058bp.txt -rw-rw-r-- 1 ps ps 180 4月 29 09:48 group33_17780926bp.txt -rw-rw-r-- 1 ps ps 152 4月 29 09:48 group3_38952077bp.txt -rw-rw-r-- 1 ps ps 243 4月 29 09:48 group34_17501202bp.txt -rw-rw-r-- 1 ps ps 152 4月 29 09:48 group35_17396856bp.txt -rw-rw-r-- 1 ps ps 208 4月 29 09:48 group36_17321984bp.txt -rw-rw-r-- 1 ps ps 88 4月 29 09:48 group37_16929067bp.txt -rw-rw-r-- 1 ps ps 119 4月 29 09:48 group38_16284770bp.txt -rw-rw-r-- 1 ps ps 119 4月 29 09:48 group39_14358708bp.txt -rw-rw-r-- 1 ps ps 88 4月 29 09:48 group40_13554138bp.txt -rw-rw-r-- 1 ps ps 270 4月 29 09:48 group41_12117333bp.txt -rw-rw-r-- 1 ps ps 148 4月 29 09:48 group42_9552907bp.txt -rw-rw-r-- 1 ps ps 247 4月 29 09:48 group4_37334910bp.txt -rw-rw-r-- 1 ps ps 88 4月 29 09:48 group43_9118406bp.txt -rw-rw-r-- 1 ps ps 88 4月 29 09:48 group44_8370283bp.txt -rw-rw-r-- 1 ps ps 245 4月 29 09:48 group5_36935828bp.txt -rw-rw-r-- 1 ps ps 216 4月 29 09:48 group6_34040223bp.txt -rw-rw-r-- 1 ps ps 216 4月 29 09:48 group7_33466005bp.txt -rw-rw-r-- 1 ps ps 152 4月 29 09:48 group8_33337447bp.txt -rw-rw-r-- 1 ps ps 369 4月 29 09:48 group9_32236358bp.txt I found that the contigs have been clustered into 44 groups. However, when I perform the second step of reassignment, I found that only 39 groups are redirected in the final_groups, which is not consistent with the expected 44 groups. How can I solve this problem?