Does hifiasm support the assembly of haploid genomes larger than 10G using HiC data?

[wjx121]

Does hifiasm support the assembly of haploid genomes larger than 10G using HiC data? I have been using my own data to assemble a genome (~15G), and the genotyping process has taken a very long time (over a month) without any results. My server cluster has 2T of memory, and I believe this should not be a limitation caused by hardware conditions.

[chhylp123]

If it is a haploid genome, please just run it without HiC using --l0. If the coverage is not too high, 2TB RAM might work.

[HuiyangYu]

Does hifiasm support the assembly of haploid genomes larger than 10G using HiC data? I have been using my own data to assemble a genome (~15G), and the genotyping process has taken a very long time (over a month) without any results. My server cluster has 2T of memory, and I believe this should not be a limitation caused by hardware conditions.

For a 15 Gb genome, without the UL ONT reads, assembly can be completed in approximately two days using 50 threads. If your sequencing depth is excessively high, you may consider downsampling the HiFi data to 50-60X. Additionally, you may want to examine the software's log files for further insights.

[wjx121]

Thank you for sharing your experience, I have also tested the assembly of HiFi data without using HiC data, which took a total of two days (this is in line with your experience). But when I add HiC data to assemble it, it's just like my initial question. The following is the information at the end of the log file at that time.

[M::ha_ct_shrink::170062.66454.61] ==> counted 633026861 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 23893930611 minimizers
[M::ha_pt_gen::173273.28754.39] ==> indexed 23889178613 positions, counted 633026861 distinct minimizer k-mers
[M::ha_print_ovlp_stat_0] # overlaps: 2919674196
[M::ha_print_ovlp_stat_0] # strong overlaps: 1097287130
[M::ha_print_ovlp_stat_0] # weak overlaps: 1822387066
[M::ha_print_ovlp_stat_0] # exact overlaps: 2650184321
[M::ha_print_ovlp_stat_0] # inexact overlaps: 269489875
[M::ha_print_ovlp_stat_0] # overlaps without large indels: 2899192894
[M::ha_print_ovlp_stat_0] # reverse overlaps: 816242957
[M::ha_print_ovlp_stat_0] # running time: 11443.071
[M::ha_assemble::184755.180*[email protected]] ==> found overlaps for the final round
[M::ha_opt_update_cov_min] updated max_n_chain to 345
Writing reads to disk...
Reads has been written.
Writing ma_hit_ts to disk...
ma_hit_ts has been written.
Writing ma_hit_ts to disk...
ma_hit_ts has been written.
bin files have been written.
[M::gen_telo_end_t::] ==> # 5'-telomeres::0, # 3'-telomeres::2, # tot::54843938, motif::TTTAGGG, motif_len::7
ERROR6
ERROR6
ERROR6
ERROR6
[M::ug_ext_gfa::] # tips::1800
Writing raw unitig GFA to disk...
ERROR6
ERROR6
Writing processed unitig GFA to disk...
ERROR6
ERROR6
[M::purge_dups] homozygous read coverage threshold: 56
[M::purge_dups] purge duplication coverage threshold: 70
ERROR-purge
[M::mc_solve:: # edges: 20450]
[M::mc_solve_core_adv::2.853] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [47, infinity]
Writing MD3.hic.p_ctg.gfa to disk...
[M::ha_opt_update_cov] updated max_n_chain to 345
ERROR6
ERROR6