No k-mer peak

[JChenGatersleben]

Hi, Haoyu and Heng:

I am running the assembly of a plant species (genome size: ~900 Mb), we used ~35x HiFi reads but the assembly is terrible (N50=600 kb, longest contig=5 Mb). So I checked the log file and I found that there is no k-mer peak as followed.

Is it indicateing that there are a lot of low-copies contaminated reads? Can we removed these HiFi reads and then run Hifiasm?
Other suggestion?

Many thanks!

Here is my log file:
job_4358018.log

[JChenGatersleben]

[M::ha_analyze_count] lowest: count[9] = 20031848
[M::ha_analyze_count] highest: count[10] = 20154211
[M::ha_hist_line] 2: ****************************************************************************************************> 45316034
[M::ha_hist_line] 3: ****************************************************************************************************> 31140378
[M::ha_hist_line] 4: ****************************************************************************************************> 25668487
[M::ha_hist_line] 5: ****************************************************************************************************> 22687300
[M::ha_hist_line] 6: ****************************************************************************************************> 21421006
[M::ha_hist_line] 7: *************************************************************************************************> 20580472
[M::ha_hist_line] 8: **************************************************************************************************** 20238770
[M::ha_hist_line] 9: *************************************************************************************************** 20031848
[M::ha_hist_line] 10: **************************************************************************************************** 20154211
[M::ha_hist_line] 11: **************************************************************************************************** 20144529
[M::ha_hist_line] 12: *************************************************************************************************** 19958354
[M::ha_hist_line] 13: ************************************************************************************************* 19599832
[M::ha_hist_line] 14: ************************************************************************************************ 19353257
[M::ha_hist_line] 15: ********************************************************************************************** 18906668
[M::ha_hist_line] 16: ******************************************************************************************** 18519423
[M::ha_hist_line] 17: ***************************************************************************************** 17870082
[M::ha_hist_line] 18: ************************************************************************************** 17277869
[M::ha_hist_line] 19: ********************************************************************************** 16598560
[M::ha_hist_line] 20: ****************************************************************************** 15815290
[M::ha_hist_line] 21: ************************************************************************** 14945205
[M::ha_hist_line] 22: ********************************************************************** 14148773
[M::ha_hist_line] 23: ****************************************************************** 13324449
[M::ha_hist_line] 24: *************************************************************** 12652378
[M::ha_hist_line] 25: ********************************************************** 11780558
[M::ha_hist_line] 26: ******************************************************* 11029135
[M::ha_hist_line] 27: *************************************************** 10239004
[M::ha_hist_line] 28: *********************************************** 9485935
[M::ha_hist_line] 29: ******************************************** 8809226
[M::ha_hist_line] 30: ***************************************** 8212016
[M::ha_hist_line] 31: ************************************** 7755655
[M::ha_hist_line] 32: ************************************ 7257639
[M::ha_hist_line] 33: ********************************** 6752401
[M::ha_hist_line] 34: ******************************* 6225899
[M::ha_hist_line] 35: ***************************** 5780716
[M::ha_hist_line] 36: *************************** 5442240
[M::ha_hist_line] 37: ************************* 5080903
[M::ha_hist_line] 38: ************************ 4745775
[M::ha_hist_line] 39: ********************** 4424617
[M::ha_hist_line] 40: ********************* 4156126
[M::ha_hist_line] 41: ******************* 3887200
[M::ha_hist_line] 42: ****************** 3618169
[M::ha_hist_line] 43: ***************** 3364025
[M::ha_hist_line] 44: **************** 3135980
[M::ha_hist_line] 45: ************** 2921741
[M::ha_hist_line] 46: ************** 2722952
[M::ha_hist_line] 47: ************* 2543319
[M::ha_hist_line] 48: ************ 2403438
[M::ha_hist_line] 49: *********** 2248962
[M::ha_hist_line] 50: ********** 2106954
[M::ha_hist_line] 51: ********** 1980467
[M::ha_hist_line] 52: ********* 1820532
[M::ha_hist_line] 53: ******** 1684849
[M::ha_hist_line] 54: ******** 1562189
[M::ha_hist_line] 55: ******* 1450614
[M::ha_hist_line] 56: ******* 1341935
[M::ha_hist_line] 57: ****** 1252736
[M::ha_hist_line] 58: ****** 1147735
[M::ha_hist_line] 59: ***** 1056606
[M::ha_hist_line] 60: ***** 979534
[M::ha_hist_line] 61: **** 903965
[M::ha_hist_line] 62: **** 833732
[M::ha_hist_line] 63: **** 765746
[M::ha_hist_line] 64: *** 703710
[M::ha_hist_line] 65: *** 650098
[M::ha_hist_line] 66: *** 606621
[M::ha_hist_line] 67: *** 557854
[M::ha_hist_line] 68: *** 515291
[M::ha_hist_line] 69: ** 474640
[M::ha_hist_line] 70: ** 435380
[M::ha_hist_line] 71: ** 408963
[M::ha_hist_line] 72: ** 372582
[M::ha_hist_line] 73: ** 344286
[M::ha_hist_line] 74: ** 312680
[M::ha_hist_line] 75: * 292491
[M::ha_hist_line] 76: * 273458
[M::ha_hist_line] 77: * 253854
[M::ha_hist_line] 78: * 238759
[M::ha_hist_line] 79: * 222127
[M::ha_hist_line] 80: * 208548
[M::ha_hist_line] 81: * 195329
[M::ha_hist_line] 82: * 186122
[M::ha_hist_line] 83: * 177918
[M::ha_hist_line] 84: * 170074
[M::ha_hist_line] 85: * 168279
[M::ha_hist_line] 86: * 163286
[M::ha_hist_line] 87: * 157398
[M::ha_hist_line] 88: * 151067
[M::ha_hist_line] 89: * 145593
[M::ha_hist_line] 90: * 142387
[M::ha_hist_line] 91: * 136372
[M::ha_hist_line] 92: * 133455
[M::ha_hist_line] 93: * 127244
[M::ha_hist_line] 94: * 123114
[M::ha_hist_line] 95: * 116818
[M::ha_hist_line] 96: * 109292
[M::ha_hist_line] 97: * 105486
[M::ha_hist_line] 98: * 102993
[M::ha_hist_line] rest: **************************************** 7975860
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_ft_gen] peak_hom: 10; peak_het: -1
[M::ha_ct_shrink::1863.8848.27] ==> counted 36347023 distinct minimizer k-mers
[M::ha_ft_gen::1881.5628.20@24.739GB] ==> filtered out 36347023 k-mers occurring 50 or more times
[M::ha_opt_update_cov] updated max_n_chain to 100
[M::yak_count] collected 597384327 minimizers
[M::ha_pt_gen::2707.6718.75] ==> counted 61521469 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[9] = 1044557
[M::ha_analyze_count] highest: count[10] = 1046579
[M::ha_hist_line] 1: ****************************************************************************************************> 27004553
[M::ha_hist_line] 2: ****************************************************************************************************> 3318415
[M::ha_hist_line] 3: ****************************************************************************************************> 1986619
[M::ha_hist_line] 4: ****************************************************************************************************> 1517595
[M::ha_hist_line] 5: ****************************************************************************************************> 1277454
[M::ha_hist_line] 6: ****************************************************************************************************> 1166770
[M::ha_hist_line] 7: ****************************************************************************************************> 1098242
[M::ha_hist_line] 8: ************************************************************************************************> 1065544
[M::ha_hist_line] 9: **************************************************************************************************** 1044557
[M::ha_hist_line] 10: **************************************************************************************************** 1046579
[M::ha_hist_line] 11: *************************************************************************************************** 1040110
[M::ha_hist_line] 12: ************************************************************************************************** 1029583
[M::ha_hist_line] 13: ************************************************************************************************* 1013573
[M::ha_hist_line] 14: *********************************************************************************************** 999206
[M::ha_hist_line] 15: ********************************************************************************************* 976813
[M::ha_hist_line] 16: ******************************************************************************************* 957344
[M::ha_hist_line] 17: ***************************************************************************************** 928629
[M::ha_hist_line] 18: *************************************************************************************** 905367
[M::ha_hist_line] 19: ************************************************************************************ 875184
[M::ha_hist_line] 20: ******************************************************************************** 839315
[M::ha_hist_line] 21: ***************************************************************************** 802077
[M::ha_hist_line] 22: ************************************************************************* 768329
[M::ha_hist_line] 23: ********************************************************************** 735678
[M::ha_hist_line] 24: ******************************************************************* 705978
[M::ha_hist_line] 25: **************************************************************** 666501
[M::ha_hist_line] 26: ************************************************************ 632572
[M::ha_hist_line] 27: ********************************************************* 593761
[M::ha_hist_line] 28: ***************************************************** 557545
[M::ha_hist_line] 29: ************************************************** 521029
[M::ha_hist_line] 30: *********************************************** 489392
[M::ha_hist_line] 31: ******************************************** 460244
[M::ha_hist_line] 32: ***************************************** 428546
[M::ha_hist_line] 33: ************************************** 394600
[M::ha_hist_line] 34: *********************************** 363559
[M::ha_hist_line] 35: ******************************** 334662
[M::ha_hist_line] 36: ****************************** 310545
[M::ha_hist_line] 37: *************************** 286979
[M::ha_hist_line] 38: ************************* 264228
[M::ha_hist_line] 39: *********************** 244269
[M::ha_hist_line] 40: ********************** 226243
[M::ha_hist_line] 41: ******************** 211191
[M::ha_hist_line] 42: ******************* 195368
[M::ha_hist_line] 43: ***************** 180683
[M::ha_hist_line] 44: **************** 167334
[M::ha_hist_line] 45: *************** 157340
[M::ha_hist_line] 46: ************** 148808
[M::ha_hist_line] 47: ************** 144495
[M::ha_hist_line] 48: *************** 153265
[M::ha_hist_line] 49: **************** 167934
[M::ha_hist_line] 50: * 12287
[M::ha_hist_line] 51: * 8994
[M::ha_hist_line] 52: * 7898
[M::ha_hist_line] 53: * 7053
[M::ha_hist_line] 54: * 6394
[M::ha_hist_line] 55: * 5854
[M::ha_hist_line] rest: ******* 68382
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 10; peak_het: -1
[M::ha_ct_shrink::2708.1978.75] ==> counted 34516916 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 597384327 minimizers
[M::ha_pt_gen::3154.0649.80] ==> indexed 570379774 positions, counted 34516916 distinct minimizer k-mers
[M::ha_assemble::9503.43521.63@24.739GB] ==> corrected reads for round 1
[M::ha_assemble] # bases: 30191922339; # corrected bases: 71955717; # recorrected bases: 71837
[M::ha_assemble] size of buffer: 4.163GB
[M::yak_count] collected 582740067 minimizers
[M::ha_pt_gen::9873.03421.51] ==> counted 38667748 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[9] = 974783
[M::ha_analyze_count] highest: count[11] = 988533
[M::ha_hist_line] 1: ****************************************************************************************************> 6606398
[M::ha_hist_line] 2: ****************************************************************************************************> 2015721
[M::ha_hist_line] 3: ****************************************************************************************************> 1471879
[M::ha_hist_line] 4: ****************************************************************************************************> 1279183
[M::ha_hist_line] 5: ****************************************************************************************************> 1127566
[M::ha_hist_line] 6: ****************************************************************************************************> 1052404
[M::ha_hist_line] 7: ************************************************************************************************> 1007493
[M::ha_hist_line] 8: **************************************************************************************************** 993238
[M::ha_hist_line] 9: *************************************************************************************************** 974783
[M::ha_hist_line] 10: **************************************************************************************************** 988117
[M::ha_hist_line] 11: **************************************************************************************************** 988533
[M::ha_hist_line] 12: **************************************************************************************************** 985265
[M::ha_hist_line] 13: *************************************************************************************************** 978278
[M::ha_hist_line] 14: ************************************************************************************************** 969006
[M::ha_hist_line] 15: ************************************************************************************************ 950359
[M::ha_hist_line] 16: *********************************************************************************************** 934877
[M::ha_hist_line] 17: ******************************************************************************************** 910821
[M::ha_hist_line] 18: ****************************************************************************************** 891002
[M::ha_hist_line] 19: *************************************************************************************** 862776
[M::ha_hist_line] 20: ************************************************************************************ 835057
[M::ha_hist_line] 21: ********************************************************************************* 799568
[M::ha_hist_line] 22: ***************************************************************************** 763610
[M::ha_hist_line] 23: ************************************************************************** 732305
[M::ha_hist_line] 24: ************************************************************************ 706968
[M::ha_hist_line] 25: ******************************************************************** 669638
[M::ha_hist_line] 26: ***************************************************************** 638059
[M::ha_hist_line] 27: ************************************************************* 603633
[M::ha_hist_line] 28: ********************************************************* 565724
[M::ha_hist_line] 29: ****************************************************** 533490
[M::ha_hist_line] 30: ************************************************** 498198
[M::ha_hist_line] 31: ************************************************ 473212
[M::ha_hist_line] 32: ********************************************* 443507
[M::ha_hist_line] 33: ****************************************** 412355
[M::ha_hist_line] 34: ************************************** 379928
[M::ha_hist_line] 35: *********************************** 348113
[M::ha_hist_line] 36: ********************************* 325993
[M::ha_hist_line] 37: ******************************* 301689
[M::ha_hist_line] 38: **************************** 277541
[M::ha_hist_line] 39: ************************** 257604
[M::ha_hist_line] 40: ************************ 237971
[M::ha_hist_line] 41: ********************** 221598
[M::ha_hist_line] 42: ********************* 205926
[M::ha_hist_line] 43: ******************* 190794
[M::ha_hist_line] 44: ****************** 175926
[M::ha_hist_line] 45: ***************** 163396
[M::ha_hist_line] 46: *************** 153176
[M::ha_hist_line] 47: ************** 142438
[M::ha_hist_line] 48: ************** 133721
[M::ha_hist_line] 49: ************* 132811
[M::ha_hist_line] 50: ************ 116030
[M::ha_hist_line] 51: ******* 72482
[M::ha_hist_line] 52: **** 36675
[M::ha_hist_line] 53: ** 19406
[M::ha_hist_line] 54: * 12576
[M::ha_hist_line] 55: * 9426
[M::ha_hist_line] 56: * 7920
[M::ha_hist_line] 57: * 6916
[M::ha_hist_line] 58: * 6017
[M::ha_hist_line] 59: * 5272
[M::ha_hist_line] rest: ****** 63380
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 11; peak_het: -1
[M::ha_ct_shrink::9873.36321.51] ==> counted 32061350 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 582740067 minimizers
[M::ha_pt_gen::10334.91921.24] ==> indexed 576133669 positions, counted 32061350 distinct minimizer k-mers
[M::ha_assemble::15342.22723.82@24.739GB] ==> corrected reads for round 2
[M::ha_assemble] # bases: 30181471385; # corrected bases: 5130409; # recorrected bases: 40046
[M::ha_assemble] size of buffer: 3.589GB
[M::yak_count] collected 580617062 minimizers
[M::ha_pt_gen::15706.21223.69] ==> counted 37014446 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[9] = 967584
[M::ha_analyze_count] highest: count[12] = 984133
[M::ha_hist_line] 1: ****************************************************************************************************> 5348300
[M::ha_hist_line] 2: ****************************************************************************************************> 1832032
[M::ha_hist_line] 3: ****************************************************************************************************> 1387663
[M::ha_hist_line] 4: ****************************************************************************************************> 1235714
[M::ha_hist_line] 5: ****************************************************************************************************> 1102020
[M::ha_hist_line] 6: ****************************************************************************************************> 1035273
[M::ha_hist_line] 7: ************************************************************************************************> 995381
[M::ha_hist_line] 8: **************************************************************************************************** 983917
[M::ha_hist_line] 9: ************************************************************************************************** 967584
[M::ha_hist_line] 10: **************************************************************************************************** 982390
[M::ha_hist_line] 11: **************************************************************************************************** 982439
[M::ha_hist_line] 12: **************************************************************************************************** 984133
[M::ha_hist_line] 13: *************************************************************************************************** 974594
[M::ha_hist_line] 14: ************************************************************************************************** 966026
[M::ha_hist_line] 15: ************************************************************************************************ 949293
[M::ha_hist_line] 16: *********************************************************************************************** 933747
[M::ha_hist_line] 17: ******************************************************************************************** 909602
[M::ha_hist_line] 18: ****************************************************************************************** 889372
[M::ha_hist_line] 19: **************************************************************************************** 861542
[M::ha_hist_line] 20: ************************************************************************************* 834612
[M::ha_hist_line] 21: ********************************************************************************* 799068
[M::ha_hist_line] 22: ***************************************************************************** 762430
[M::ha_hist_line] 23: ************************************************************************** 732419
[M::ha_hist_line] 24: ************************************************************************ 706106
[M::ha_hist_line] 25: ******************************************************************** 668611
[M::ha_hist_line] 26: ***************************************************************** 639020
[M::ha_hist_line] 27: ************************************************************* 603960
[M::ha_hist_line] 28: ********************************************************* 565795
[M::ha_hist_line] 29: ****************************************************** 534168
[M::ha_hist_line] 30: *************************************************** 498188
[M::ha_hist_line] 31: ************************************************ 473957
[M::ha_hist_line] 32: ********************************************* 443390
[M::ha_hist_line] 33: ****************************************** 413838
[M::ha_hist_line] 34: *************************************** 380753
[M::ha_hist_line] 35: *********************************** 349056
[M::ha_hist_line] 36: ********************************* 326293
[M::ha_hist_line] 37: ******************************* 301744
[M::ha_hist_line] 38: **************************** 278280
[M::ha_hist_line] 39: ************************** 258161
[M::ha_hist_line] 40: ************************ 237960
[M::ha_hist_line] 41: *********************** 222129
[M::ha_hist_line] 42: ********************* 206541
[M::ha_hist_line] 43: ******************* 191188
[M::ha_hist_line] 44: ****************** 176517
[M::ha_hist_line] 45: ***************** 164205
[M::ha_hist_line] 46: **************** 152984
[M::ha_hist_line] 47: ************** 142702
[M::ha_hist_line] 48: ************** 134006
[M::ha_hist_line] 49: ************* 131577
[M::ha_hist_line] 50: ************ 116502
[M::ha_hist_line] 51: ******** 74613
[M::ha_hist_line] 52: **** 38196
[M::ha_hist_line] 53: ** 20478
[M::ha_hist_line] 54: * 13214
[M::ha_hist_line] 55: * 9793
[M::ha_hist_line] 56: * 8175
[M::ha_hist_line] 57: * 6879
[M::ha_hist_line] 58: * 6186
[M::ha_hist_line] 59: * 5402
[M::ha_hist_line] 60: * 4967
[M::ha_hist_line] rest: ****** 59361
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 12; peak_het: -1
[M::ha_ct_shrink::15706.38423.69] ==> counted 31666146 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 580617062 minimizers
[M::ha_pt_gen::16139.80723.49] ==> indexed 575268762 positions, counted 31666146 distinct minimizer k-mers
[M::ha_assemble::21512.85224.21@26.139GB] ==> corrected reads for round 3
[M::ha_assemble] # bases: 30180475913; # corrected bases: 1188922; # recorrected bases: 35730
[M::ha_assemble] size of buffer: 3.610GB
[M::yak_count] collected 579912840 minimizers
[M::ha_pt_gen::21885.20724.11] ==> counted 36616479 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[9] = 965378
[M::ha_analyze_count] highest: count[12] = 983403
[M::ha_hist_line] 1: ****************************************************************************************************> 5100322
[M::ha_hist_line] 2: ****************************************************************************************************> 1758291
[M::ha_hist_line] 3: ****************************************************************************************************> 1354910
[M::ha_hist_line] 4: ****************************************************************************************************> 1220035
[M::ha_hist_line] 5: ****************************************************************************************************> 1093808
[M::ha_hist_line] 6: ****************************************************************************************************> 1029829
[M::ha_hist_line] 7: *************************************************************************************************> 991360
[M::ha_hist_line] 8: **************************************************************************************************** 981083
[M::ha_hist_line] 9: ************************************************************************************************** 965378
[M::ha_hist_line] 10: **************************************************************************************************** 980783
[M::ha_hist_line] 11: **************************************************************************************************** 981228
[M::ha_hist_line] 12: **************************************************************************************************** 983403
[M::ha_hist_line] 13: *************************************************************************************************** 973537
[M::ha_hist_line] 14: ************************************************************************************************** 965793
[M::ha_hist_line] 15: ************************************************************************************************ 948676
[M::ha_hist_line] 16: *********************************************************************************************** 933379
[M::ha_hist_line] 17: ******************************************************************************************** 909281
[M::ha_hist_line] 18: ****************************************************************************************** 889323
[M::ha_hist_line] 19: **************************************************************************************** 861564
[M::ha_hist_line] 20: ************************************************************************************* 834349
[M::ha_hist_line] 21: ********************************************************************************* 798932
[M::ha_hist_line] 22: ****************************************************************************** 762431
[M::ha_hist_line] 23: ************************************************************************** 732432
[M::ha_hist_line] 24: ************************************************************************ 706363
[M::ha_hist_line] 25: ******************************************************************** 668372
[M::ha_hist_line] 26: ***************************************************************** 638834
[M::ha_hist_line] 27: ************************************************************* 604059
[M::ha_hist_line] 28: ********************************************************** 565947
[M::ha_hist_line] 29: ****************************************************** 534238
[M::ha_hist_line] 30: *************************************************** 498319
[M::ha_hist_line] 31: ************************************************ 473971
[M::ha_hist_line] 32: ********************************************* 443219
[M::ha_hist_line] 33: ****************************************** 414119
[M::ha_hist_line] 34: *************************************** 380775
[M::ha_hist_line] 35: *********************************** 348821
[M::ha_hist_line] 36: ********************************* 326494
[M::ha_hist_line] 37: ******************************* 301785
[M::ha_hist_line] 38: **************************** 278441
[M::ha_hist_line] 39: ************************** 258190
[M::ha_hist_line] 40: ************************ 237896
[M::ha_hist_line] 41: *********************** 222145
[M::ha_hist_line] 42: ********************* 206514
[M::ha_hist_line] 43: ******************* 191328
[M::ha_hist_line] 44: ****************** 176445
[M::ha_hist_line] 45: ***************** 164296
[M::ha_hist_line] 46: **************** 153006
[M::ha_hist_line] 47: *************** 142703
[M::ha_hist_line] 48: ************** 134003
[M::ha_hist_line] 49: ************* 131658
[M::ha_hist_line] 50: ************ 116532
[M::ha_hist_line] 51: ******** 74743
[M::ha_hist_line] 52: **** 38254
[M::ha_hist_line] 53: ** 20536
[M::ha_hist_line] 54: * 13321
[M::ha_hist_line] 55: * 9868
[M::ha_hist_line] 56: * 8177
[M::ha_hist_line] 57: * 6957
[M::ha_hist_line] 58: * 6181
[M::ha_hist_line] 59: * 5371
[M::ha_hist_line] 60: * 4975
[M::ha_hist_line] rest: ****** 59496
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 12; peak_het: -1
[M::ha_ct_shrink::21885.42024.11] ==> counted 31516157 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 579912840 minimizers
[M::ha_pt_gen::22332.54823.94] ==> indexed 574812518 positions, counted 31516157 distinct minimizer k-mers
[M::ha_assemble::23188.46024.15@27.066GB] ==> found overlaps for the final round
[M::ha_print_ovlp_stat] # overlaps: 77473298
[M::ha_print_ovlp_stat] # strong overlaps: 30875553
[M::ha_print_ovlp_stat] # weak overlaps: 46597745
[M::ha_print_ovlp_stat] # exact overlaps: 71031631
[M::ha_print_ovlp_stat] # inexact overlaps: 6441667
[M::ha_print_ovlp_stat] # overlaps without large indels: 77098860
[M::ha_print_ovlp_stat] # reverse overlaps: 20716919
[M::ha_opt_update_cov_min] updated max_n_chain to 100
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: 32
[M::purge_dups] purge duplication coverage threshold: 40
[M::ug_ext_gfa::] # tips::2933
Writing raw unitig GFA to disk...
[M::ug_ext_gfa::] # tips::5
Writing processed unitig GFA to disk...
[M::purge_dups] homozygous read coverage threshold: 32
[M::purge_dups] purge duplication coverage threshold: 40
[M::mc_solve:: # edges: 15824]
[M::mc_solve_core_adv::2.908] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [27, infinity]
Writing Chamae_30G.bp.p_ctg.gfa to disk...
[M::adjust_utg_by_trio] primary contig coverage range: [27, infinity]
Writing Chamae_30G.bp.hap1.p_ctg.gfa to disk...
[M::adjust_utg_by_trio] primary contig coverage range: [27, infinity]
Writing Chamae_30G.bp.hap2.p_ctg.gfa to disk...
Inconsistency threshold for low-quality regions in BED files: 70%
[M::main] Version: 0.19.3-r572
[M::main] CMD: /filer-5/agruppen/CSF/Jianyong_Chen/Hifiasm/hifiasm/hifiasm -o Chamae_30G -t 60 /hsm/lims/CSF/PACBIO/2023/230123_073223/ccs/houben/3048470/m54203Ue_230123_073223_094/m54203Ue_230123_073223.hifi_reads.fastq.gz
[M::main] Real time: 24276.488 sec; CPU: 561405.912 sec; Peak RSS: 27.066 GB

[chhylp123]

It might be a common issue for the iput data (see: https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash);

[JChenGatersleben]

Thanks a lot!