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kmer null #745

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AlcaArctica opened this issue Dec 17, 2024 · 1 comment
Open

kmer null #745

AlcaArctica opened this issue Dec 17, 2024 · 1 comment

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@AlcaArctica
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AlcaArctica commented Dec 17, 2024 •
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I have been running hifiasm successfully for some time. However, yesterday I got a very strange result for two birds (another bird species assembled just fine). Here is the example for one of the species:

hifiasm result files:

0	bpacvit.a_ctg.fasta
0	bpacvit.a_ctg.gfa
0	bpacvit.a_ctg.lowQ.bed
0	bpacvit.a_ctg.noseq.gfa
16G	bpacvit.ec.bin
12G	bpacvit.ovlp.reverse.bin
51G	bpacvit.ovlp.source.bin
128K	bpacvit.p_ctg.fasta
128K	bpacvit.p_ctg.gfa
0	bpacvit.p_ctg.lowQ.bed
512	bpacvit.p_ctg.noseq.gfa
128K	bpacvit.p_utg.gfa
0	bpacvit.p_utg.lowQ.bed
512	bpacvit.p_utg.noseq.gfa
128K	bpacvit.r_utg.gfa
0	bpacvit.r_utg.lowQ.bed
512	bpacvit.r_utg.noseq.gfa
0	hifiasm_done.flag
64K	hifiasm.log

hifiasm.log file:

[M::ha_analyze_count] lowest: count[199] = 0
[M::ha_analyze_count] highest: count[200] = 86137742
[M::ha_hist_line]     2:  0
[M::ha_hist_line]     3:  0
[M::ha_hist_line]     4:  0
[M::ha_hist_line]     5:  0
[M::ha_hist_line]     6:  0
[M::ha_hist_line]     7:  0
[M::ha_hist_line]     8:  0
[M::ha_hist_line]     9:  0
[M::ha_hist_line]    10:  0
[M::ha_hist_line]    11:  0
[M::ha_hist_line]    12:  0
[M::ha_hist_line]    13:  0
[M::ha_hist_line]    14:  0
[M::ha_hist_line]    15:  0
[M::ha_hist_line]    16:  0
[M::ha_hist_line]    17:  0
[M::ha_hist_line]    18:  0
[M::ha_hist_line]    19:  0
[M::ha_hist_line]    20:  0
[M::ha_hist_line]    21:  0
[M::ha_hist_line]    22:  0
[M::ha_hist_line]    23:  0
[M::ha_hist_line]    24:  0
[M::ha_hist_line]    25:  0
[M::ha_hist_line]    26:  0
[M::ha_hist_line]    27:  0
[M::ha_hist_line]    28:  0
[M::ha_hist_line]    29:  0
[M::ha_hist_line]    30:  0
[M::ha_hist_line]    31:  0
[M::ha_hist_line]    32:  0
[M::ha_hist_line]    33:  0
[M::ha_hist_line]    34:  0
[M::ha_hist_line]    35:  0
[M::ha_hist_line]    36:  0
[M::ha_hist_line]    37:  0
[M::ha_hist_line]    38:  0
[M::ha_hist_line]    39:  0
[M::ha_hist_line]    40:  0
[M::ha_hist_line]    41:  0
[M::ha_hist_line]    42:  0
[M::ha_hist_line]    43:  0
[M::ha_hist_line]    44:  0
[M::ha_hist_line]    45:  0
[M::ha_hist_line]    46:  0
[M::ha_hist_line]    47:  0
[M::ha_hist_line]    48:  0
[M::ha_hist_line]    49:  0
[M::ha_hist_line]    50:  0
[M::ha_hist_line]    51:  0
[M::ha_hist_line]    52:  0
[M::ha_hist_line]    53:  0
[M::ha_hist_line]    54:  0
[M::ha_hist_line]    55:  0
[M::ha_hist_line]    56:  0
[M::ha_hist_line]    57:  0
[M::ha_hist_line]    58:  0
[M::ha_hist_line]    59:  0
[M::ha_hist_line]    60:  0
[M::ha_hist_line]    61:  0
[M::ha_hist_line]    62:  0
[M::ha_hist_line]    63:  0
[M::ha_hist_line]    64:  0
[M::ha_hist_line]    65:  0
[M::ha_hist_line]    66:  0
[M::ha_hist_line]    67:  0
[M::ha_hist_line]    68:  0
[M::ha_hist_line]    69:  0
[M::ha_hist_line]    70:  0
[M::ha_hist_line]    71:  0
[M::ha_hist_line]    72:  0
[M::ha_hist_line]    73:  0
[M::ha_hist_line]    74:  0
[M::ha_hist_line]    75:  0
[M::ha_hist_line]    76:  0
[M::ha_hist_line]    77:  0
[M::ha_hist_line]    78:  0
[M::ha_hist_line]    79:  0
[M::ha_hist_line]    80:  0
[M::ha_hist_line]    81:  0
[M::ha_hist_line]    82:  0
[M::ha_hist_line]    83:  0
[M::ha_hist_line]    84:  0
[M::ha_hist_line]    85:  0
[M::ha_hist_line]    86:  0
[M::ha_hist_line]    87:  0
[M::ha_hist_line]    88:  0
[M::ha_hist_line]    89:  0
[M::ha_hist_line]    90:  0
[M::ha_hist_line]    91:  0
[M::ha_hist_line]    92:  0
[M::ha_hist_line]    93:  0
[M::ha_hist_line]    94:  0
[M::ha_hist_line]    95:  0
[M::ha_hist_line]    96:  0
[M::ha_hist_line]    97:  0
[M::ha_hist_line]    98:  0
[M::ha_hist_line]    99:  0
[M::ha_hist_line]   100:  0
[M::ha_hist_line]   101:  0
[M::ha_hist_line]   102:  0
[M::ha_hist_line]   103:  0
[M::ha_hist_line]   104:  0
[M::ha_hist_line]   105:  0
[M::ha_hist_line]   106:  0
[M::ha_hist_line]   107:  0
[M::ha_hist_line]   108:  0
[M::ha_hist_line]   109:  0
[M::ha_hist_line]   110:  0
[M::ha_hist_line]   111:  0
[M::ha_hist_line]   112:  0
[M::ha_hist_line]   113:  0
[M::ha_hist_line]   114:  0
[M::ha_hist_line]   115:  0
[M::ha_hist_line]   116:  0
[M::ha_hist_line]   117:  0
[M::ha_hist_line]   118:  0
[M::ha_hist_line]   119:  0
[M::ha_hist_line]   120:  0
[M::ha_hist_line]   121:  0
[M::ha_hist_line]   122:  0
[M::ha_hist_line]   123:  0
[M::ha_hist_line]   124:  0
[M::ha_hist_line]   125:  0
[M::ha_hist_line]   126:  0
[M::ha_hist_line]   127:  0
[M::ha_hist_line]   128:  0
[M::ha_hist_line]   129:  0
[M::ha_hist_line]   130:  0
[M::ha_hist_line]   131:  0
[M::ha_hist_line]   132:  0
[M::ha_hist_line]   133:  0
[M::ha_hist_line]   134:  0
[M::ha_hist_line]   135:  0
[M::ha_hist_line]   136:  0
[M::ha_hist_line]   137:  0
[M::ha_hist_line]   138:  0
[M::ha_hist_line]   139:  0
[M::ha_hist_line]   140:  0
[M::ha_hist_line]   141:  0
[M::ha_hist_line]   142:  0
[M::ha_hist_line]   143:  0
[M::ha_hist_line]   144:  0
[M::ha_hist_line]   145:  0
[M::ha_hist_line]   146:  0
[M::ha_hist_line]   147:  0
[M::ha_hist_line]   148:  0
[M::ha_hist_line]   149:  0
[M::ha_hist_line]   150:  0
[M::ha_hist_line]   151:  0
[M::ha_hist_line]   152:  0
[M::ha_hist_line]   153:  0
[M::ha_hist_line]   154:  0
[M::ha_hist_line]   155:  0
[M::ha_hist_line]   156:  0
[M::ha_hist_line]   157:  0
[M::ha_hist_line]   158:  0
[M::ha_hist_line]   159:  0
[M::ha_hist_line]   160:  0
[M::ha_hist_line]   161:  0
[M::ha_hist_line]   162:  0
[M::ha_hist_line]   163:  0
[M::ha_hist_line]   164:  0
[M::ha_hist_line]   165:  0
[M::ha_hist_line]   166:  0
[M::ha_hist_line]   167:  0
[M::ha_hist_line]   168:  0
[M::ha_hist_line]   169:  0
[M::ha_hist_line]   170:  0
[M::ha_hist_line]   171:  0
[M::ha_hist_line]   172:  0
[M::ha_hist_line]   173:  0
[M::ha_hist_line]   174:  0
[M::ha_hist_line]   175:  0
[M::ha_hist_line]   176:  0
[M::ha_hist_line]   177:  0
[M::ha_hist_line]   178:  0
[M::ha_hist_line]   179:  0
[M::ha_hist_line]   180:  0
[M::ha_hist_line]   181:  0
[M::ha_hist_line]   182:  0
[M::ha_hist_line]   183:  0
[M::ha_hist_line]   184:  0
[M::ha_hist_line]   185:  0
[M::ha_hist_line]   186:  0
[M::ha_hist_line]   187:  0
[M::ha_hist_line]   188:  0
[M::ha_hist_line]   189:  0
[M::ha_hist_line]   190:  0
[M::ha_hist_line]   191:  0
[M::ha_hist_line]   192:  0
[M::ha_hist_line]   193:  0
[M::ha_hist_line]   194:  0
[M::ha_hist_line]   195:  0
[M::ha_hist_line]   196:  0
[M::ha_hist_line]   197:  0
[M::ha_hist_line]   198:  0
[M::ha_hist_line]   199:  0
[M::ha_hist_line]   200: **************************************************************************************************** 86137742
[M::ha_hist_line]  rest: ********************************************************************************************* 80491369
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: count[300] = 64464420
[M::ha_ft_gen] peak_hom: 300; peak_het: 200
[M::ha_ct_shrink::1017.471*10.44] ==> counted 33781 distinct minimizer k-mers
[M::ha_ft_gen::1017.847*[email protected]] ==> filtered out 33781 k-mers occurring 4094 or more times
[M::ha_opt_update_cov] updated max_n_chain to 6000
[M::yak_count] collected 1750512500 minimizers
[M::ha_pt_gen::2024.783*7.39] ==> counted 6470925 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[199] = 0
[M::ha_analyze_count] highest: count[200] = 3350272
[M::ha_hist_line]     2:  0
[M::ha_hist_line]     3:  0
[M::ha_hist_line]     4:  0
[M::ha_hist_line]     5:  0
[M::ha_hist_line]     6:  0
[M::ha_hist_line]     7:  0
[M::ha_hist_line]     8:  0
[M::ha_hist_line]     9:  0
[M::ha_hist_line]    10:  0
[M::ha_hist_line]    11:  0
[M::ha_hist_line]    12:  0
[M::ha_hist_line]    13:  0
[M::ha_hist_line]    14:  0
[M::ha_hist_line]    15:  0
[M::ha_hist_line]    16:  0
[M::ha_hist_line]    17:  0
[M::ha_hist_line]    18:  0
[M::ha_hist_line]    19:  0
[M::ha_hist_line]    20:  0
[M::ha_hist_line]    21:  0
[M::ha_hist_line]    22:  0
[M::ha_hist_line]    23:  0
[M::ha_hist_line]    24:  0
[M::ha_hist_line]    25:  0
[M::ha_hist_line]    26:  0
[M::ha_hist_line]    27:  0
[M::ha_hist_line]    28:  0
[M::ha_hist_line]    29:  0
[M::ha_hist_line]    30:  0
[M::ha_hist_line]    31:  0
[M::ha_hist_line]    32:  0
[M::ha_hist_line]    33:  0
[M::ha_hist_line]    34:  0
[M::ha_hist_line]    35:  0
[M::ha_hist_line]    36:  0
[M::ha_hist_line]    37:  0
[M::ha_hist_line]    38:  0
[M::ha_hist_line]    39:  0
[M::ha_hist_line]    40:  0
[M::ha_hist_line]    41:  0
[M::ha_hist_line]    42:  0
[M::ha_hist_line]    43:  0
[M::ha_hist_line]    44:  0
[M::ha_hist_line]    45:  0
[M::ha_hist_line]    46:  0
[M::ha_hist_line]    47:  0
[M::ha_hist_line]    48:  0
[M::ha_hist_line]    49:  0
[M::ha_hist_line]    50:  0
[M::ha_hist_line]    51:  0
[M::ha_hist_line]    52:  0
[M::ha_hist_line]    53:  0
[M::ha_hist_line]    54:  0
[M::ha_hist_line]    55:  0
[M::ha_hist_line]    56:  0
[M::ha_hist_line]    57:  0
[M::ha_hist_line]    58:  0
[M::ha_hist_line]    59:  0
[M::ha_hist_line]    60:  0
[M::ha_hist_line]    61:  0
[M::ha_hist_line]    62:  0
[M::ha_hist_line]    63:  0
[M::ha_hist_line]    64:  0
[M::ha_hist_line]    65:  0
[M::ha_hist_line]    66:  0
[M::ha_hist_line]    67:  0
[M::ha_hist_line]    68:  0
[M::ha_hist_line]    69:  0
[M::ha_hist_line]    70:  0
[M::ha_hist_line]    71:  0
[M::ha_hist_line]    72:  0
[M::ha_hist_line]    73:  0
[M::ha_hist_line]    74:  0
[M::ha_hist_line]    75:  0
[M::ha_hist_line]    76:  0
[M::ha_hist_line]    77:  0
[M::ha_hist_line]    78:  0
[M::ha_hist_line]    79:  0
[M::ha_hist_line]    80:  0
[M::ha_hist_line]    81:  0
[M::ha_hist_line]    82:  0
[M::ha_hist_line]    83:  0
[M::ha_hist_line]    84:  0
[M::ha_hist_line]    85:  0
[M::ha_hist_line]    86:  0
[M::ha_hist_line]    87:  0
[M::ha_hist_line]    88:  0
[M::ha_hist_line]    89:  0
[M::ha_hist_line]    90:  0
[M::ha_hist_line]    91:  0
[M::ha_hist_line]    92:  0
[M::ha_hist_line]    93:  0
[M::ha_hist_line]    94:  0
[M::ha_hist_line]    95:  0
[M::ha_hist_line]    96:  0
[M::ha_hist_line]    97:  0
[M::ha_hist_line]    98:  0
[M::ha_hist_line]    99:  0
[M::ha_hist_line]   100:  0
[M::ha_hist_line]   101:  0
[M::ha_hist_line]   102:  0
[M::ha_hist_line]   103:  0
[M::ha_hist_line]   104:  0
[M::ha_hist_line]   105:  0
[M::ha_hist_line]   106:  0
[M::ha_hist_line]   107:  0
[M::ha_hist_line]   108:  0
[M::ha_hist_line]   109:  0
[M::ha_hist_line]   110:  0
[M::ha_hist_line]   111:  0
[M::ha_hist_line]   112:  0
[M::ha_hist_line]   113:  0
[M::ha_hist_line]   114:  0
[M::ha_hist_line]   115:  0
[M::ha_hist_line]   116:  0
[M::ha_hist_line]   117:  0
[M::ha_hist_line]   118:  0
[M::ha_hist_line]   119:  0
[M::ha_hist_line]   120:  0
[M::ha_hist_line]   121:  0
[M::ha_hist_line]   122:  0
[M::ha_hist_line]   123:  0
[M::ha_hist_line]   124:  0
[M::ha_hist_line]   125:  0
[M::ha_hist_line]   126:  0
[M::ha_hist_line]   127:  0
[M::ha_hist_line]   128:  0
[M::ha_hist_line]   129:  0
[M::ha_hist_line]   130:  0
[M::ha_hist_line]   131:  0
[M::ha_hist_line]   132:  0
[M::ha_hist_line]   133:  0
[M::ha_hist_line]   134:  0
[M::ha_hist_line]   135:  0
[M::ha_hist_line]   136:  0
[M::ha_hist_line]   137:  0
[M::ha_hist_line]   138:  0
[M::ha_hist_line]   139:  0
[M::ha_hist_line]   140:  0
[M::ha_hist_line]   141:  0
[M::ha_hist_line]   142:  0
[M::ha_hist_line]   143:  0
[M::ha_hist_line]   144:  0
[M::ha_hist_line]   145:  0
[M::ha_hist_line]   146:  0
[M::ha_hist_line]   147:  0
[M::ha_hist_line]   148:  0
[M::ha_hist_line]   149:  0
[M::ha_hist_line]   150:  0
[M::ha_hist_line]   151:  0
[M::ha_hist_line]   152:  0
[M::ha_hist_line]   153:  0
[M::ha_hist_line]   154:  0
[M::ha_hist_line]   155:  0
[M::ha_hist_line]   156:  0
[M::ha_hist_line]   157:  0
[M::ha_hist_line]   158:  0
[M::ha_hist_line]   159:  0
[M::ha_hist_line]   160:  0
[M::ha_hist_line]   161:  0
[M::ha_hist_line]   162:  0
[M::ha_hist_line]   163:  0
[M::ha_hist_line]   164:  0
[M::ha_hist_line]   165:  0
[M::ha_hist_line]   166:  0
[M::ha_hist_line]   167:  0
[M::ha_hist_line]   168:  0
[M::ha_hist_line]   169:  0
[M::ha_hist_line]   170:  0
[M::ha_hist_line]   171:  0
[M::ha_hist_line]   172:  0
[M::ha_hist_line]   173:  0
[M::ha_hist_line]   174:  0
[M::ha_hist_line]   175:  0
[M::ha_hist_line]   176:  0
[M::ha_hist_line]   177:  0
[M::ha_hist_line]   178:  0
[M::ha_hist_line]   179:  0
[M::ha_hist_line]   180:  0
[M::ha_hist_line]   181:  0
[M::ha_hist_line]   182:  0
[M::ha_hist_line]   183:  0
[M::ha_hist_line]   184:  0
[M::ha_hist_line]   185:  0
[M::ha_hist_line]   186:  0
[M::ha_hist_line]   187:  0
[M::ha_hist_line]   188:  0
[M::ha_hist_line]   189:  0
[M::ha_hist_line]   190:  0
[M::ha_hist_line]   191:  0
[M::ha_hist_line]   192:  0
[M::ha_hist_line]   193:  0
[M::ha_hist_line]   194:  0
[M::ha_hist_line]   195:  0
[M::ha_hist_line]   196:  0
[M::ha_hist_line]   197:  0
[M::ha_hist_line]   198:  0
[M::ha_hist_line]   199:  0
[M::ha_hist_line]   200: **************************************************************************************************** 3350272
[M::ha_hist_line]  rest: ********************************************************************************************* 3120653
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: count[300] = 2506575
[M::ha_pt_gen] peak_hom: 300; peak_het: 200
[M::ha_ct_shrink::2024.802*7.39] ==> counted 6470925 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1750512500 minimizers
[M::ha_pt_gen::2115.219*8.80] ==> indexed 1750512500 positions, counted 6470925 distinct minimizer k-mers
[M::pec::6764.410] # bases: 64580432600; # corrected bases: 2133000
[M::ha_assemble::8884.867*[email protected]] ==> corrected reads for round 1
[M::ha_assemble] # bases: 64580432600; # corrected bases: 2133000
[M::yak_count] collected 1750514900 minimizers
[M::ha_pt_gen::8965.583*56.62] ==> counted 6470317 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[199] = 0
[M::ha_analyze_count] highest: count[200] = 3349553
[M::ha_hist_line]     2:  0
[M::ha_hist_line]     3:  0
[M::ha_hist_line]     4:  0
[M::ha_hist_line]     5:  0
[M::ha_hist_line]     6:  0
[M::ha_hist_line]     7:  0
[M::ha_hist_line]     8:  0
[M::ha_hist_line]     9:  0
[M::ha_hist_line]    10:  0
[M::ha_hist_line]    11:  0
[M::ha_hist_line]    12:  0
[M::ha_hist_line]    13:  0
[M::ha_hist_line]    14:  0
[M::ha_hist_line]    15:  0
[M::ha_hist_line]    16:  0
[M::ha_hist_line]    17:  0
[M::ha_hist_line]    18:  0
[M::ha_hist_line]    19:  0
[M::ha_hist_line]    20:  0
[M::ha_hist_line]    21:  0
[M::ha_hist_line]    22:  0
[M::ha_hist_line]    23:  0
[M::ha_hist_line]    24:  0
[M::ha_hist_line]    25:  0
[M::ha_hist_line]    26:  0
[M::ha_hist_line]    27:  0
[M::ha_hist_line]    28:  0
[M::ha_hist_line]    29:  0
[M::ha_hist_line]    30:  0
[M::ha_hist_line]    31:  0
[M::ha_hist_line]    32:  0
[M::ha_hist_line]    33:  0
[M::ha_hist_line]    34:  0
[M::ha_hist_line]    35:  0
[M::ha_hist_line]    36:  0
[M::ha_hist_line]    37:  0
[M::ha_hist_line]    38:  0
[M::ha_hist_line]    39:  0
[M::ha_hist_line]    40:  0
[M::ha_hist_line]    41:  0
[M::ha_hist_line]    42:  0
[M::ha_hist_line]    43:  0
[M::ha_hist_line]    44:  0
[M::ha_hist_line]    45:  0
[M::ha_hist_line]    46:  0
[M::ha_hist_line]    47:  0
[M::ha_hist_line]    48:  0
[M::ha_hist_line]    49:  0
[M::ha_hist_line]    50:  0
[M::ha_hist_line]    51:  0
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[M::ha_hist_line]    54:  0
[M::ha_hist_line]    55:  0
[M::ha_hist_line]    56:  0
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[M::ha_hist_line]    58:  0
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[M::ha_hist_line]    60:  0
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[M::ha_hist_line]    78:  0
[M::ha_hist_line]    79:  0
[M::ha_hist_line]    80:  0
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[M::ha_hist_line]    82:  0
[M::ha_hist_line]    83:  0
[M::ha_hist_line]    84:  0
[M::ha_hist_line]    85:  0
[M::ha_hist_line]    86:  0
[M::ha_hist_line]    87:  0
[M::ha_hist_line]    88:  0
[M::ha_hist_line]    89:  0
[M::ha_hist_line]    90:  0
[M::ha_hist_line]    91:  0
[M::ha_hist_line]    92:  0
[M::ha_hist_line]    93:  0
[M::ha_hist_line]    94:  0
[M::ha_hist_line]    95:  0
[M::ha_hist_line]    96:  0
[M::ha_hist_line]    97:  0
[M::ha_hist_line]    98:  0
[M::ha_hist_line]    99:  0
[M::ha_hist_line]   100:  0
[M::ha_hist_line]   101:  0
[M::ha_hist_line]   102:  0
[M::ha_hist_line]   103:  0
[M::ha_hist_line]   104:  0
[M::ha_hist_line]   105:  0
[M::ha_hist_line]   106:  0
[M::ha_hist_line]   107:  0
[M::ha_hist_line]   108:  0
[M::ha_hist_line]   109:  0
[M::ha_hist_line]   110:  0
[M::ha_hist_line]   111:  0
[M::ha_hist_line]   112:  0
[M::ha_hist_line]   113:  0
[M::ha_hist_line]   114:  0
[M::ha_hist_line]   115:  0
[M::ha_hist_line]   116:  0
[M::ha_hist_line]   117:  0
[M::ha_hist_line]   118:  0
[M::ha_hist_line]   119:  0
[M::ha_hist_line]   120:  0
[M::ha_hist_line]   121:  0
[M::ha_hist_line]   122:  0
[M::ha_hist_line]   123:  0
[M::ha_hist_line]   124:  0
[M::ha_hist_line]   125:  0
[M::ha_hist_line]   126:  0
[M::ha_hist_line]   127:  0
[M::ha_hist_line]   128:  0
[M::ha_hist_line]   129:  0
[M::ha_hist_line]   130:  0
[M::ha_hist_line]   131:  0
[M::ha_hist_line]   132:  0
[M::ha_hist_line]   133:  0
[M::ha_hist_line]   134:  0
[M::ha_hist_line]   135:  0
[M::ha_hist_line]   136:  0
[M::ha_hist_line]   137:  0
[M::ha_hist_line]   138:  0
[M::ha_hist_line]   139:  0
[M::ha_hist_line]   140:  0
[M::ha_hist_line]   141:  0
[M::ha_hist_line]   142:  0
[M::ha_hist_line]   143:  0
[M::ha_hist_line]   144:  0
[M::ha_hist_line]   145:  0
[M::ha_hist_line]   146:  0
[M::ha_hist_line]   147:  0
[M::ha_hist_line]   148:  0
[M::ha_hist_line]   149:  0
[M::ha_hist_line]   150:  0
[M::ha_hist_line]   151:  0
[M::ha_hist_line]   152:  0
[M::ha_hist_line]   153:  0
[M::ha_hist_line]   154:  0
[M::ha_hist_line]   155:  0
[M::ha_hist_line]   156:  0
[M::ha_hist_line]   157:  0
[M::ha_hist_line]   158:  0
[M::ha_hist_line]   159:  0
[M::ha_hist_line]   160:  0
[M::ha_hist_line]   161:  0
[M::ha_hist_line]   162:  0
[M::ha_hist_line]   163:  0
[M::ha_hist_line]   164:  0
[M::ha_hist_line]   165:  0
[M::ha_hist_line]   166:  0
[M::ha_hist_line]   167:  0
[M::ha_hist_line]   168:  0
[M::ha_hist_line]   169:  0
[M::ha_hist_line]   170:  0
[M::ha_hist_line]   171:  0
[M::ha_hist_line]   172:  0
[M::ha_hist_line]   173:  0
[M::ha_hist_line]   174:  0
[M::ha_hist_line]   175:  0
[M::ha_hist_line]   176:  0
[M::ha_hist_line]   177:  0
[M::ha_hist_line]   178:  0
[M::ha_hist_line]   179:  0
[M::ha_hist_line]   180:  0
[M::ha_hist_line]   181:  0
[M::ha_hist_line]   182:  0
[M::ha_hist_line]   183:  0
[M::ha_hist_line]   184:  0
[M::ha_hist_line]   185:  0
[M::ha_hist_line]   186:  0
[M::ha_hist_line]   187:  0
[M::ha_hist_line]   188:  0
[M::ha_hist_line]   189:  0
[M::ha_hist_line]   190:  0
[M::ha_hist_line]   191:  0
[M::ha_hist_line]   192:  0
[M::ha_hist_line]   193:  0
[M::ha_hist_line]   194:  0
[M::ha_hist_line]   195:  0
[M::ha_hist_line]   196:  0
[M::ha_hist_line]   197:  0
[M::ha_hist_line]   198:  0
[M::ha_hist_line]   199:  0
[M::ha_hist_line]   200: **************************************************************************************************** 3349553
[M::ha_hist_line]  rest: ********************************************************************************************* 3120764
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: count[300] = 2506111
[M::ha_pt_gen] peak_hom: 300; peak_het: 200
[M::ha_ct_shrink::8965.669*56.62] ==> counted 6470317 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1750514900 minimizers
[M::ha_pt_gen::9054.940*56.46] ==> indexed 1750514900 positions, counted 6470317 distinct minimizer k-mers
[M::pec::4410.005] # bases: 64581686000; # corrected bases: 92700
[M::ha_assemble::13469.633*[email protected]] ==> corrected reads for round 2
[M::ha_assemble] # bases: 64581686000; # corrected bases: 92700
[M::yak_count] collected 1750515300 minimizers
[M::ha_pt_gen::13550.001*61.35] ==> counted 6470276 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[199] = 0
[M::ha_analyze_count] highest: count[200] = 3349513
[M::ha_hist_line]     2:  0
[M::ha_hist_line]     3:  0
[M::ha_hist_line]     4:  0
[M::ha_hist_line]     5:  0
[M::ha_hist_line]     6:  0
[M::ha_hist_line]     7:  0
[M::ha_hist_line]     8:  0
[M::ha_hist_line]     9:  0
[M::ha_hist_line]    10:  0
[M::ha_hist_line]    11:  0
[M::ha_hist_line]    12:  0
[M::ha_hist_line]    13:  0
[M::ha_hist_line]    14:  0
[M::ha_hist_line]    15:  0
[M::ha_hist_line]    16:  0
[M::ha_hist_line]    17:  0
[M::ha_hist_line]    18:  0
[M::ha_hist_line]    19:  0
[M::ha_hist_line]    20:  0
[M::ha_hist_line]    21:  0
[M::ha_hist_line]    22:  0
[M::ha_hist_line]    23:  0
[M::ha_hist_line]    24:  0
[M::ha_hist_line]    25:  0
[M::ha_hist_line]    26:  0
[M::ha_hist_line]    27:  0
[M::ha_hist_line]    28:  0
[M::ha_hist_line]    29:  0
[M::ha_hist_line]    30:  0
[M::ha_hist_line]    31:  0
[M::ha_hist_line]    32:  0
[M::ha_hist_line]    33:  0
[M::ha_hist_line]    34:  0
[M::ha_hist_line]    35:  0
[M::ha_hist_line]    36:  0
[M::ha_hist_line]    37:  0
[M::ha_hist_line]    38:  0
[M::ha_hist_line]    39:  0
[M::ha_hist_line]    40:  0
[M::ha_hist_line]    41:  0
[M::ha_hist_line]    42:  0
[M::ha_hist_line]    43:  0
[M::ha_hist_line]    44:  0
[M::ha_hist_line]    45:  0
[M::ha_hist_line]    46:  0
[M::ha_hist_line]    47:  0
[M::ha_hist_line]    48:  0
[M::ha_hist_line]    49:  0
[M::ha_hist_line]    50:  0
[M::ha_hist_line]    51:  0
[M::ha_hist_line]    52:  0
[M::ha_hist_line]    53:  0
[M::ha_hist_line]    54:  0
[M::ha_hist_line]    55:  0
[M::ha_hist_line]    56:  0
[M::ha_hist_line]    57:  0
[M::ha_hist_line]    58:  0
[M::ha_hist_line]    59:  0
[M::ha_hist_line]    60:  0
[M::ha_hist_line]    61:  0
[M::ha_hist_line]    62:  0
[M::ha_hist_line]    63:  0
[M::ha_hist_line]    64:  0
[M::ha_hist_line]    65:  0
[M::ha_hist_line]    66:  0
[M::ha_hist_line]    67:  0
[M::ha_hist_line]    68:  0
[M::ha_hist_line]    69:  0
[M::ha_hist_line]    70:  0
[M::ha_hist_line]    71:  0
[M::ha_hist_line]    72:  0
[M::ha_hist_line]    73:  0
[M::ha_hist_line]    74:  0
[M::ha_hist_line]    75:  0
[M::ha_hist_line]    76:  0
[M::ha_hist_line]    77:  0
[M::ha_hist_line]    78:  0
[M::ha_hist_line]    79:  0
[M::ha_hist_line]    80:  0
[M::ha_hist_line]    81:  0
[M::ha_hist_line]    82:  0
[M::ha_hist_line]    83:  0
[M::ha_hist_line]    84:  0
[M::ha_hist_line]    85:  0
[M::ha_hist_line]    86:  0
[M::ha_hist_line]    87:  0
[M::ha_hist_line]    88:  0
[M::ha_hist_line]    89:  0
[M::ha_hist_line]    90:  0
[M::ha_hist_line]    91:  0
[M::ha_hist_line]    92:  0
[M::ha_hist_line]    93:  0
[M::ha_hist_line]    94:  0
[M::ha_hist_line]    95:  0
[M::ha_hist_line]    96:  0
[M::ha_hist_line]    97:  0
[M::ha_hist_line]    98:  0
[M::ha_hist_line]    99:  0
[M::ha_hist_line]   100:  0
[M::ha_hist_line]   101:  0
[M::ha_hist_line]   102:  0
[M::ha_hist_line]   103:  0
[M::ha_hist_line]   104:  0
[M::ha_hist_line]   105:  0
[M::ha_hist_line]   106:  0
[M::ha_hist_line]   107:  0
[M::ha_hist_line]   108:  0
[M::ha_hist_line]   109:  0
[M::ha_hist_line]   110:  0
[M::ha_hist_line]   111:  0
[M::ha_hist_line]   112:  0
[M::ha_hist_line]   113:  0
[M::ha_hist_line]   114:  0
[M::ha_hist_line]   115:  0
[M::ha_hist_line]   116:  0
[M::ha_hist_line]   117:  0
[M::ha_hist_line]   118:  0
[M::ha_hist_line]   119:  0
[M::ha_hist_line]   120:  0
[M::ha_hist_line]   121:  0
[M::ha_hist_line]   122:  0
[M::ha_hist_line]   123:  0
[M::ha_hist_line]   124:  0
[M::ha_hist_line]   125:  0
[M::ha_hist_line]   126:  0
[M::ha_hist_line]   127:  0
[M::ha_hist_line]   128:  0
[M::ha_hist_line]   129:  0
[M::ha_hist_line]   130:  0
[M::ha_hist_line]   131:  0
[M::ha_hist_line]   132:  0
[M::ha_hist_line]   133:  0
[M::ha_hist_line]   134:  0
[M::ha_hist_line]   135:  0
[M::ha_hist_line]   136:  0
[M::ha_hist_line]   137:  0
[M::ha_hist_line]   138:  0
[M::ha_hist_line]   139:  0
[M::ha_hist_line]   140:  0
[M::ha_hist_line]   141:  0
[M::ha_hist_line]   142:  0
[M::ha_hist_line]   143:  0
[M::ha_hist_line]   144:  0
[M::ha_hist_line]   145:  0
[M::ha_hist_line]   146:  0
[M::ha_hist_line]   147:  0
[M::ha_hist_line]   148:  0
[M::ha_hist_line]   149:  0
[M::ha_hist_line]   150:  0
[M::ha_hist_line]   151:  0
[M::ha_hist_line]   152:  0
[M::ha_hist_line]   153:  0
[M::ha_hist_line]   154:  0
[M::ha_hist_line]   155:  0
[M::ha_hist_line]   156:  0
[M::ha_hist_line]   157:  0
[M::ha_hist_line]   158:  0
[M::ha_hist_line]   159:  0
[M::ha_hist_line]   160:  0
[M::ha_hist_line]   161:  0
[M::ha_hist_line]   162:  0
[M::ha_hist_line]   163:  0
[M::ha_hist_line]   164:  0
[M::ha_hist_line]   165:  0
[M::ha_hist_line]   166:  0
[M::ha_hist_line]   167:  0
[M::ha_hist_line]   168:  0
[M::ha_hist_line]   169:  0
[M::ha_hist_line]   170:  0
[M::ha_hist_line]   171:  0
[M::ha_hist_line]   172:  0
[M::ha_hist_line]   173:  0
[M::ha_hist_line]   174:  0
[M::ha_hist_line]   175:  0
[M::ha_hist_line]   176:  0
[M::ha_hist_line]   177:  0
[M::ha_hist_line]   178:  0
[M::ha_hist_line]   179:  0
[M::ha_hist_line]   180:  0
[M::ha_hist_line]   181:  0
[M::ha_hist_line]   182:  0
[M::ha_hist_line]   183:  0
[M::ha_hist_line]   184:  0
[M::ha_hist_line]   185:  0
[M::ha_hist_line]   186:  0
[M::ha_hist_line]   187:  0
[M::ha_hist_line]   188:  0
[M::ha_hist_line]   189:  0
[M::ha_hist_line]   190:  0
[M::ha_hist_line]   191:  0
[M::ha_hist_line]   192:  0
[M::ha_hist_line]   193:  0
[M::ha_hist_line]   194:  0
[M::ha_hist_line]   195:  0
[M::ha_hist_line]   196:  0
[M::ha_hist_line]   197:  0
[M::ha_hist_line]   198:  0
[M::ha_hist_line]   199:  0
[M::ha_hist_line]   200: **************************************************************************************************** 3349513
[M::ha_hist_line]  rest: ********************************************************************************************* 3120763
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: count[300] = 2506070
[M::ha_pt_gen] peak_hom: 300; peak_het: 200
[M::ha_ct_shrink::13550.030*61.35] ==> counted 6470276 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1750515300 minimizers
[M::ha_pt_gen::13637.925*61.22] ==> indexed 1750515300 positions, counted 6470276 distinct minimizer k-mers
[M::pec::4116.487] # bases: 64581743900; # corrected bases: 1900
[M::ha_assemble::17829.150*[email protected]] ==> corrected reads for round 3
[M::ha_assemble] # bases: 64581743900; # corrected bases: 1900
[M::yak_count] collected 1750516000 minimizers
[M::ha_pt_gen::17914.181*63.58] ==> counted 6470276 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[199] = 0
[M::ha_analyze_count] highest: count[200] = 3349515
[M::ha_hist_line]     2:  0
[M::ha_hist_line]     3:  0
[M::ha_hist_line]     4:  0
[M::ha_hist_line]     5:  0
[M::ha_hist_line]     6:  0
[M::ha_hist_line]     7:  0
[M::ha_hist_line]     8:  0
[M::ha_hist_line]     9:  0
[M::ha_hist_line]    10:  0
[M::ha_hist_line]    11:  0
[M::ha_hist_line]    12:  0
[M::ha_hist_line]    13:  0
[M::ha_hist_line]    14:  0
[M::ha_hist_line]    15:  0
[M::ha_hist_line]    16:  0
[M::ha_hist_line]    17:  0
[M::ha_hist_line]    18:  0
[M::ha_hist_line]    19:  0
[M::ha_hist_line]    20:  0
[M::ha_hist_line]    21:  0
[M::ha_hist_line]    22:  0
[M::ha_hist_line]    23:  0
[M::ha_hist_line]    24:  0
[M::ha_hist_line]    25:  0
[M::ha_hist_line]    26:  0
[M::ha_hist_line]    27:  0
[M::ha_hist_line]    28:  0
[M::ha_hist_line]    29:  0
[M::ha_hist_line]    30:  0
[M::ha_hist_line]    31:  0
[M::ha_hist_line]    32:  0
[M::ha_hist_line]    33:  0
[M::ha_hist_line]    34:  0
[M::ha_hist_line]    35:  0
[M::ha_hist_line]    36:  0
[M::ha_hist_line]    37:  0
[M::ha_hist_line]    38:  0
[M::ha_hist_line]    39:  0
[M::ha_hist_line]    40:  0
[M::ha_hist_line]    41:  0
[M::ha_hist_line]    42:  0
[M::ha_hist_line]    43:  0
[M::ha_hist_line]    44:  0
[M::ha_hist_line]    45:  0
[M::ha_hist_line]    46:  0
[M::ha_hist_line]    47:  0
[M::ha_hist_line]    48:  0
[M::ha_hist_line]    49:  0
[M::ha_hist_line]    50:  0
[M::ha_hist_line]    51:  0
[M::ha_hist_line]    52:  0
[M::ha_hist_line]    53:  0
[M::ha_hist_line]    54:  0
[M::ha_hist_line]    55:  0
[M::ha_hist_line]    56:  0
[M::ha_hist_line]    57:  0
[M::ha_hist_line]    58:  0
[M::ha_hist_line]    59:  0
[M::ha_hist_line]    60:  0
[M::ha_hist_line]    61:  0
[M::ha_hist_line]    62:  0
[M::ha_hist_line]    63:  0
[M::ha_hist_line]    64:  0
[M::ha_hist_line]    65:  0
[M::ha_hist_line]    66:  0
[M::ha_hist_line]    67:  0
[M::ha_hist_line]    68:  0
[M::ha_hist_line]    69:  0
[M::ha_hist_line]    70:  0
[M::ha_hist_line]    71:  0
[M::ha_hist_line]    72:  0
[M::ha_hist_line]    73:  0
[M::ha_hist_line]    74:  0
[M::ha_hist_line]    75:  0
[M::ha_hist_line]    76:  0
[M::ha_hist_line]    77:  0
[M::ha_hist_line]    78:  0
[M::ha_hist_line]    79:  0
[M::ha_hist_line]    80:  0
[M::ha_hist_line]    81:  0
[M::ha_hist_line]    82:  0
[M::ha_hist_line]    83:  0
[M::ha_hist_line]    84:  0
[M::ha_hist_line]    85:  0
[M::ha_hist_line]    86:  0
[M::ha_hist_line]    87:  0
[M::ha_hist_line]    88:  0
[M::ha_hist_line]    89:  0
[M::ha_hist_line]    90:  0
[M::ha_hist_line]    91:  0
[M::ha_hist_line]    92:  0
[M::ha_hist_line]    93:  0
[M::ha_hist_line]    94:  0
[M::ha_hist_line]    95:  0
[M::ha_hist_line]    96:  0
[M::ha_hist_line]    97:  0
[M::ha_hist_line]    98:  0
[M::ha_hist_line]    99:  0
[M::ha_hist_line]   100:  0
[M::ha_hist_line]   101:  0
[M::ha_hist_line]   102:  0
[M::ha_hist_line]   103:  0
[M::ha_hist_line]   104:  0
[M::ha_hist_line]   105:  0
[M::ha_hist_line]   106:  0
[M::ha_hist_line]   107:  0
[M::ha_hist_line]   108:  0
[M::ha_hist_line]   109:  0
[M::ha_hist_line]   110:  0
[M::ha_hist_line]   111:  0
[M::ha_hist_line]   112:  0
[M::ha_hist_line]   113:  0
[M::ha_hist_line]   114:  0
[M::ha_hist_line]   115:  0
[M::ha_hist_line]   116:  0
[M::ha_hist_line]   117:  0
[M::ha_hist_line]   118:  0
[M::ha_hist_line]   119:  0
[M::ha_hist_line]   120:  0
[M::ha_hist_line]   121:  0
[M::ha_hist_line]   122:  0
[M::ha_hist_line]   123:  0
[M::ha_hist_line]   124:  0
[M::ha_hist_line]   125:  0
[M::ha_hist_line]   126:  0
[M::ha_hist_line]   127:  0
[M::ha_hist_line]   128:  0
[M::ha_hist_line]   129:  0
[M::ha_hist_line]   130:  0
[M::ha_hist_line]   131:  0
[M::ha_hist_line]   132:  0
[M::ha_hist_line]   133:  0
[M::ha_hist_line]   134:  0
[M::ha_hist_line]   135:  0
[M::ha_hist_line]   136:  0
[M::ha_hist_line]   137:  0
[M::ha_hist_line]   138:  0
[M::ha_hist_line]   139:  0
[M::ha_hist_line]   140:  0
[M::ha_hist_line]   141:  0
[M::ha_hist_line]   142:  0
[M::ha_hist_line]   143:  0
[M::ha_hist_line]   144:  0
[M::ha_hist_line]   145:  0
[M::ha_hist_line]   146:  0
[M::ha_hist_line]   147:  0
[M::ha_hist_line]   148:  0
[M::ha_hist_line]   149:  0
[M::ha_hist_line]   150:  0
[M::ha_hist_line]   151:  0
[M::ha_hist_line]   152:  0
[M::ha_hist_line]   153:  0
[M::ha_hist_line]   154:  0
[M::ha_hist_line]   155:  0
[M::ha_hist_line]   156:  0
[M::ha_hist_line]   157:  0
[M::ha_hist_line]   158:  0
[M::ha_hist_line]   159:  0
[M::ha_hist_line]   160:  0
[M::ha_hist_line]   161:  0
[M::ha_hist_line]   162:  0
[M::ha_hist_line]   163:  0
[M::ha_hist_line]   164:  0
[M::ha_hist_line]   165:  0
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[M::ha_hist_line]   169:  0
[M::ha_hist_line]   170:  0
[M::ha_hist_line]   171:  0
[M::ha_hist_line]   172:  0
[M::ha_hist_line]   173:  0
[M::ha_hist_line]   174:  0
[M::ha_hist_line]   175:  0
[M::ha_hist_line]   176:  0
[M::ha_hist_line]   177:  0
[M::ha_hist_line]   178:  0
[M::ha_hist_line]   179:  0
[M::ha_hist_line]   180:  0
[M::ha_hist_line]   181:  0
[M::ha_hist_line]   182:  0
[M::ha_hist_line]   183:  0
[M::ha_hist_line]   184:  0
[M::ha_hist_line]   185:  0
[M::ha_hist_line]   186:  0
[M::ha_hist_line]   187:  0
[M::ha_hist_line]   188:  0
[M::ha_hist_line]   189:  0
[M::ha_hist_line]   190:  0
[M::ha_hist_line]   191:  0
[M::ha_hist_line]   192:  0
[M::ha_hist_line]   193:  0
[M::ha_hist_line]   194:  0
[M::ha_hist_line]   195:  0
[M::ha_hist_line]   196:  0
[M::ha_hist_line]   197:  0
[M::ha_hist_line]   198:  0
[M::ha_hist_line]   199:  0
[M::ha_hist_line]   200: **************************************************************************************************** 3349515
[M::ha_hist_line]  rest: ********************************************************************************************* 3120761
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: count[300] = 2506065
[M::ha_pt_gen] peak_hom: 300; peak_het: 200
[M::ha_ct_shrink::17914.204*63.58] ==> counted 6470276 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1750516000 minimizers
[M::ha_pt_gen::18004.829*63.46] ==> indexed 1750516000 positions, counted 6470276 distinct minimizer k-mers
[M::ha_print_ovlp_stat_0] # overlaps: 1298250000
[M::ha_print_ovlp_stat_0] # strong overlaps: 283866500
[M::ha_print_ovlp_stat_0] # weak overlaps: 1014383500
[M::ha_print_ovlp_stat_0] # exact overlaps: 1294790000
[M::ha_print_ovlp_stat_0] # inexact overlaps: 3460000
[M::ha_print_ovlp_stat_0] # overlaps without large indels: 1298250000
[M::ha_print_ovlp_stat_0] # reverse overlaps: 303300000
[M::ha_print_ovlp_stat_0] # running time: 1879.088
[M::ha_assemble::19886.528*[email protected]] ==> found overlaps for the final round
[M::ha_opt_update_cov_min] updated max_n_chain to 6000
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::purge_dups] homozygous read coverage threshold: 300
[M::purge_dups] purge duplication coverage threshold: 375
Writing raw unitig GFA to disk... 
Writing processed unitig GFA to disk... 
[M::purge_dups] homozygous read coverage threshold: 300
[M::purge_dups] purge duplication coverage threshold: 375
[M::mc_solve:: # edges: 0]
[M::mc_solve_core_adv::0.000] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [255, infinity]
Writing primary contig GFA to disk... 
Writing alternate contig GFA to disk... 
Inconsistency threshold for low-quality regions in BED files: 70%
[M::main] Version: 0.20.0-r639
[M::main] CMD: /raven/u/luelze/sw/hifiasm/hifiasm --primary -o bpacvit -t 72 -D 20 -N 200 /raven/ptmp/luelze/data/bPacVit/hifi/bPacVit_hifi_2combined.fastq.gz
[M::main] Real time: 24078.698 sec; CPU: 1281355.144 sec; Peak RSS: 112.237 GB

What is going on here? So my first idea of course would be that the input data is wrong. However, the normal stats for this sequence data (hifi data from a sequell machine) seem completely fine and not different from more successful assemblies.

image

I do get very strange genomescope results back though. With a very high read error rate:

linear_plot

GenomeScope version 2.0
input file = /ptmp/luelze/analysis/bPacVit/hifi/qc/reads/jellyfish/bPacVit_reads.histo
output directory = /ptmp/luelze/analysis/bPacVit/hifi/qc/reads/genomescope2/
p = 2
k = 21
max_kmercov = 10000

property                      min               max               
Homozygous (aa)               92.2701%          100%              
Heterozygous (ab)             0%                7.72991%          
Genome Haploid Length         5,072,797 bp      9,145,149 bp      
Genome Repeat Length          4,866,734 bp      8,773,662 bp      
Genome Unique Length          206,063 bp        371,487 bp        
Model Fit                     5.69873%          5.69873%          
Read Error Rate               7.09965%          7.09965%

But then the Q30 from the seqkit stats seems alright? So what is happing? Does anyone have an idea?
@HuiyangYu
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Based on the information you provided, the reads used for assembly appear to be merely a collection of reads along with their duplicates. You may need to carefully review your data.

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@AlcaArctica @HuiyangYu