Hifi + Hi-c + ONT assembly fails

[pashapu43]

Hi,

I am trying to assemble a phased genome of an outcrossing hexaploid grass species. The hybrid assembly failed with the error "hifiasm: gfa_ut.cpp:14200: uint32_t load_scaf_base(all_ul_t, char, const char*): Assertion `z->rlen == len' failed". How can i solve this issue?

SLURM output: Reads has been loaded. Loading ma_hit_ts from disk... ma_hit_ts has been read. Loading ma_hit_ts from disk... ma_hit_ts has been read. [M::ha_assemble::9085.7720.43] ==> loaded corrected reads and overlaps from disk [M::ha_opt_update_cov_min] updated max_n_chain to 485 [M::ul_load::] ==> UL [M::ha_opt_update_cov] updated max_n_chain to 485 [M::load_all_ul_t] Index has been loaded. [M::print_ovlp_src_bl_stat::] ==> # HiFi reads:45261774, # covered HiFi reads:14717015, # chained HiFi reads:7083760 [M::print_ovlp_src_bl_stat::] ==> # passed UL reads:7984626, # fully corrected UL reads:2647363, # almost fully corrected UL reads:203179, # UL reads have primary chains:3671972 [M::ha_opt_update_cov] updated max_n_chain to 485 [M::work_ul_gchains_consensus::] # try:1505671, # done:189870 [M::clean_contain_g0::] # discard cread::1628665 [M::update_sg_uo::] ==> # gfa reads:2627962, # covered gfa reads:1647747 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 485 [M::gen_cov_track::] # bases: 9688307633 [M::work_ul_gchains::] # try:3495606, # done:1957510 [M::update_sg_uo::] ==> # gfa reads:2249809, # covered gfa reads:1780796 [M::ha_opt_update_cov] updated max_n_chain to 485 [M::work_ul_gchains_consensus::] # try:14348, # done:4757 [M::clean_contain_g0::] # discard cread::797 [M::update_sg_uo::] ==> # gfa reads:2249012, # covered gfa reads:1780115 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 485 [M::gen_cov_track::] # bases: 9093435976 [M::work_ul_gchains::] # try:71449, # done:24722 [M::update_sg_uo::] ==> # gfa reads:2240747, # covered gfa reads:1778904 [M::ha_opt_update_cov] updated max_n_chain to 485 [M::work_ul_gchains_consensus::] # try:8119, # done:87 [M::clean_contain_g0::] # discard cread::26 [M::update_sg_uo::] ==> # gfa reads:2240721, # covered gfa reads:1778878 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 485 [M::gen_cov_track::] # bases: 8829104567 [M::work_ul_gchains::] # try:53722, # done:11024 [M::update_sg_uo::] ==> # gfa reads:2236753, # covered gfa reads:1778706 [M::ha_opt_update_cov] updated max_n_chain to 485 [M::work_ul_gchains_consensus::] # try:7735, # done:29 [M::clean_contain_g0::] # discard cread::7 [M::update_sg_uo::] ==> # gfa reads:2236746, # covered gfa reads:1778698 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 485 [M::gen_cov_track::] # bases: 8656540855 [M::work_ul_gchains::] # try:51916, # done:10211 [M::update_sg_uo::] ==> # gfa reads:2233435, # covered gfa reads:1778476 [M::ha_opt_update_cov] updated max_n_chain to 485 [M::work_ul_gchains_consensus::] # try:7582, # done:26 [M::clean_contain_g0::] # discard cread::3 [M::update_sg_uo::] ==> # gfa reads:2233432, # covered gfa reads:1778471 [M::ha_opt_update_cov] updated max_n_chain to 485 [M::work_ul_gchains_consensus::] # try:7527, # done:0 [M::clean_contain_g0::] # discard cread::0 [M::update_sg_uo::] ==> # gfa reads:2233431, # covered gfa reads:1778470 [M::purge_dups] homozygous read coverage threshold: 196 [M::purge_dups] purge duplication coverage threshold: 246 [M::ug_ext_gfa::] # tips::923 Writing raw unitig GFA to disk... [M::update_sg_uo::] ==> # gfa reads:2221565, # covered gfa reads:1772873 [M::ul_realignment::] ==> starting UL [M::ha_opt_update_cov] updated max_n_chain to 485 [M::load_all_ul_t] Index has been loaded. [M::print_integert_ovlp_stat::] # UL reads::16710, # UL ovlps::58752 [M::print_integert_ovlp_stat::] # UL reads::11337, # UL ovlps::19074 [M::load_all_ul_t] Index has been loaded. hifiasm: gfa_ut.cpp:14200: uint32_t load_scaf_base(all_ul_t, char, const char): Assertion `z->rlen == len' failed. /var/tmp/slurmd/job14377053/slurm_script: line 28: 21672 Aborted

[thirtykmpersecond]

I have the same problem as you. Have you solved it？

[chhylp123]

Which version are you using? Thanks!

[thirtykmpersecond]

Which version are you using? Thanks!

Version 0.19.9-r616.

SGE outputs: Reads has been loaded. Loading ma_hit_ts from disk... ma_hit_ts has been read. Loading ma_hit_ts from disk... ma_hit_ts has been read. [M::ha_assemble::250.4310.96] ==> loaded corrected reads and overlaps from disk [M::ha_opt_update_cov_min] updated max_n_chain to 455 [M::ul_load::] ==> UL [M::ha_opt_update_cov] updated max_n_chain to 455 [M::load_all_ul_t] Index has been loaded. [M::print_ovlp_src_bl_stat::] ==> # HiFi reads:5018727, # covered HiFi reads:924705, # chained HiFi reads:867647 [M::print_ovlp_src_bl_stat::] ==> # passed UL reads:325159, # fully corrected UL reads:273056, # almost fully corrected UL reads:17589, # UL reads have primary chains:34157 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:156025, # done:104113 [M::clean_contain_g0::] # discard cread::104288 [M::update_sg_uo::] ==> # gfa reads:521778, # covered gfa reads:509971 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3134227960 [M::work_ul_gchains::] # try:78651, # done:65258 [M::update_sg_uo::] ==> # gfa reads:508876, # covered gfa reads:504704 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:5074, # done:825 [M::clean_contain_g0::] # discard cread::287 [M::update_sg_uo::] ==> # gfa reads:508589, # covered gfa reads:504440 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3087888533 [M::work_ul_gchains::] # try:7789, # done:3252 [M::update_sg_uo::] ==> # gfa reads:508236, # covered gfa reads:504189 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3861, # done:34 [M::clean_contain_g0::] # discard cread::6 [M::update_sg_uo::] ==> # gfa reads:508230, # covered gfa reads:504184 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3067475553 [M::work_ul_gchains::] # try:5839, # done:1557 [M::update_sg_uo::] ==> # gfa reads:508079, # covered gfa reads:504122 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3731, # done:32 [M::clean_contain_g0::] # discard cread::4 [M::update_sg_uo::] ==> # gfa reads:508075, # covered gfa reads:504120 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3051710731 [M::work_ul_gchains::] # try:5710, # done:1494 [M::update_sg_uo::] ==> # gfa reads:507926, # covered gfa reads:504018 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3636, # done:29 [M::clean_contain_g0::] # discard cread::3 [M::update_sg_uo::] ==> # gfa reads:507923, # covered gfa reads:504015 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3594, # done:0 [M::clean_contain_g0::] # discard cread::0 [M::update_sg_uo::] ==> # gfa reads:507919, # covered gfa reads:504011 [M::purge_dups] homozygous read coverage threshold: 90 [M::purge_dups] purge duplication coverage threshold: 113 [M::ug_ext_gfa::] # tips::98 Writing raw unitig GFA to disk... [M::update_sg_uo::] ==> # gfa reads:502105, # covered gfa reads:499220 [M::ul_realignment::] ==> starting UL [M::ha_opt_update_cov] updated max_n_chain to 455 [M::load_all_ul_t] Index has been loaded. [M::print_integert_ovlp_stat::] # UL reads::131365, # UL ovlps::4137592 [M::print_integert_ovlp_stat::] # UL reads::36892, # UL ovlps::295090 [M::load_all_ul_t] Index has been loaded. hifiasm: gfa_ut.cpp:14228: uint32_t load_scaf_base(all_ul_t, char, const char): Assertion `z->rlen == len' failed.

[thirtykmpersecond]

Which version are you using? Thanks!

Version 0.19.9-r616.

SGE outputs: Reads has been loaded. Loading ma_hit_ts from disk... ma_hit_ts has been read. Loading ma_hit_ts from disk... ma_hit_ts has been read. [M::ha_assemble::250.431_0.96] ==> loaded corrected reads and overlaps from disk [M::ha_opt_update_cov_min] updated max_n_chain to 455 [M::ul_load::] ==> UL [M::ha_opt_update_cov] updated max_n_chain to 455 [M::load_all_ul_t] Index has been loaded. [M::print_ovlp_src_bl_stat::] ==> # HiFi reads:5018727, # covered HiFi reads:924705, # chained HiFi reads:867647 [M::print_ovlp_src_bl_stat::] ==> # passed UL reads:325159, # fully corrected UL reads:273056, # almost fully corrected UL reads:17589, # UL reads have primary chains:34157 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:156025, # done:104113 [M::clean_contain_g0::] # discard cread::104288 [M::update_sg_uo::] ==> # gfa reads:521778, # covered gfa reads:509971 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3134227960 [M::work_ul_gchains::] # try:78651, # done:65258 [M::update_sg_uo::] ==> # gfa reads:508876, # covered gfa reads:504704 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:5074, # done:825 [M::clean_contain_g0::] # discard cread::287 [M::update_sg_uo::] ==> # gfa reads:508589, # covered gfa reads:504440 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3087888533 [M::work_ul_gchains::] # try:7789, # done:3252 [M::update_sg_uo::] ==> # gfa reads:508236, # covered gfa reads:504189 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3861, # done:34 [M::clean_contain_g0::] # discard cread::6 [M::update_sg_uo::] ==> # gfa reads:508230, # covered gfa reads:504184 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3067475553 [M::work_ul_gchains::] # try:5839, # done:1557 [M::update_sg_uo::] ==> # gfa reads:508079, # covered gfa reads:504122 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3731, # done:32 [M::clean_contain_g0::] # discard cread::4 [M::update_sg_uo::] ==> # gfa reads:508075, # covered gfa reads:504120 [M::ul_refine_alignment::] ==> UL refinement... [M::ha_opt_update_cov] updated max_n_chain to 455 [M::gen_cov_track::] # bases: 3051710731 [M::work_ul_gchains::] # try:5710, # done:1494 [M::update_sg_uo::] ==> # gfa reads:507926, # covered gfa reads:504018 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3636, # done:29 [M::clean_contain_g0::] # discard cread::3 [M::update_sg_uo::] ==> # gfa reads:507923, # covered gfa reads:504015 [M::ha_opt_update_cov] updated max_n_chain to 455 [M::work_ul_gchains_consensus::] # try:3594, # done:0 [M::clean_contain_g0::] # discard cread::0 [M::update_sg_uo::] ==> # gfa reads:507919, # covered gfa reads:504011 [M::purge_dups] homozygous read coverage threshold: 90 [M::purge_dups] purge duplication coverage threshold: 113 [M::ug_ext_gfa::] # tips::98 Writing raw unitig GFA to disk... [M::update_sg_uo::] ==> # gfa reads:502105, # covered gfa reads:499220 [M::ul_realignment::] ==> starting UL [M::ha_opt_update_cov] updated max_n_chain to 455 [M::load_all_ul_t] Index has been loaded. [M::print_integert_ovlp_stat::] # UL reads::131365, # UL ovlps::4137592 [M::print_integert_ovlp_stat::] # UL reads::36892, # UL ovlps::295090 [M::load_all_ul_t] Index has been loaded. hifiasm: gfa_ut.cpp:14228: uint32_t load_scaf_base(all_ult, char, const char): Assertion `z->rlen == len' failed.

The program was interrupted because the storage was full. After deleting the related error files, the program runs successfully .

[chhylp123]

Ok, thanks so much!