Partition - Segmentation fault

[jlipovac]

Hi @chhylp123,

I tried to run the latest hifiasm version (0.19.8-r603) with data that I was running (successfully) with before. There is only one difference, UL reads are rebasecalled using dorado. Also, I used --dual-scaf flag. This is the end part of the log:

[M::cal_graph_ovlp_binning::321.123] ==> Qualification
[M::write_emask_t] Index has been written.
[M::rescall_ul_pipeline::1340.028] ==> Qualification
[M::rescall_ul_pipeline::] ==> # reads: 159822, # bases: 0, # fully corrected reads: 141263
[M::write_all_ul_t] Index has been written.
[M::print_integert_ovlp_stat::] # UL reads::20952, # UL ovlps::506728
[M::print_integert_ovlp_stat::] # UL reads::10522, # UL ovlps::97954
[M::load_all_ul_t] Index has been loaded.
+[M::realloc_rdb_adv] rid_n0::3721627, rid_n::3724535
-[M::realloc_rdb_adv] rid_n0::3721627, rid_n::3724535
+[M::update_paf] dn::3721627
[M::renew_ng] nocc::3724535, ng->n_seq::3724535, sg->n_seq::3721627
[M::purge_dups] homozygous read coverage threshold: 81
[M::purge_dups] purge duplication coverage threshold: 102
[M::ug_ext_gfa::] # tips::5
Writing processed unitig GFA to disk...
[M::purge_dups] homozygous read coverage threshold: 81
[M::purge_dups] purge duplication coverage threshold: 102
ERROR-purge
[M::mc_solve:: # edges: 1178]
[M::mc_solve_core_adv::0.000] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [68, infinity]
Writing /storage4/jlipovac/durian/hifiasm_assembly/durian.hifiasm.hic.ul.hic.p_ctg.gfa to disk...
[M::ha_opt_update_cov] updated max_n_chain to 410
[M::gen_trans_base_count_comp::233.794] ==> Qualification
[M::build_unitig_index::31.384] ==> Counting
[M::build_unitig_index::16.347] ==> Memory allocating
[M::build_unitig_index::51.480] ==> Filling pos
[M::build_unitig_index::0.231] ==> Sorting pos
[M::build_unitig_index::99.449] ==> HiC index has been built
[M::write_hc_pt_index] Index has been written.
[M::alignment_worker_pipeline::935.964] ==> Qualification
[M::dedup_hits::6.679] ==> Dedup
[M::dedup_hits::3.665] ==> Dedup
[M::stat] # misjoined unitigs: 9 (N50: 1334473); # corrected unitigs: 18 (N50: 961364)
[M::adjust_weight_kv_u_trans_advance::5.154]
[M::mc_solve:: # edges: 262132]
[M::mb_solve_core::0.080] ==> Partition
Segmentation fault (core dumped)

Do you have any idea what is the problem?

[chhylp123]

It might be a bug. Is it possible that you can share the bin files with me? I could fix this bug quickly.

[jlipovac]

All bin files? Let me upload it to drive then I'll send you the link.