Large Unitigs Size in Phased Assembly of Hexaploid

[dozhun]

hi, developers, I am encountering an issue during the hexaploid genome assembly except ~3G with haplotype, but the results are larger. I used 2 cells hifi reads approximately 175G driverd h Revio platform , with hifiasm-0.19.8 --primary -l0(run_1), I obtained a phased unitigs set of ~5.3G in totally, and N50 ~67K, which is much larger than expected. I also used the same data with parameters --hg-size 3G --primary --n-hap 6 --hom-cov 330 (run_2) and obtained a unitigs set of about 4.1G with N50 of ~210K, which is still much larger than expected. the genome survey from Genomescope2, the execution log and assembly graph of hifiasm, and the kat comp results as below. Please help me check if the parameters are set correctly, or suggest other solutions. Best regards, Jun hifiasm.run1.log hifiasm.run2.log run1.p_utg.noseq.gfa.zip run2.p_utg.noseq.gfa.zip