Wrong --hom-cov

[MIEFIGH]

Thank you for such an excellent assembly software.
I meeet a problem, the k-mer peak is wrong though i have setted as 60
the log is:
[M::ha_analyze_count] lowest: count[5] = 2356424
[M::ha_analyze_count] highest: count[64] = 19458901
[M::ha_hist_line] 2: ****************************************************************************************************> 29452975
[M::ha_hist_line] 3: ************************************ 6920929
[M::ha_hist_line] 4: ***************** 3230959
[M::ha_hist_line] 5: ************ 2356424
[M::ha_hist_line] 6: ************ 2374732
[M::ha_hist_line] 7: *************** 2970178
[M::ha_hist_line] 8: ******************** 3851051
[M::ha_hist_line] 9: ************************** 5030522
[M::ha_hist_line] 10: ********************************* 6349145
[M::ha_hist_line] 11: **************************************** 7795941
[M::ha_hist_line] 12: ********************************************** 9000151
[M::ha_hist_line] 13: **************************************************** 10105549
[M::ha_hist_line] 14: ******************************************************* 10768261
[M::ha_hist_line] 15: ******************************************************** 10968540
[M::ha_hist_line] 16: ******************************************************* 10756757
[M::ha_hist_line] 17: **************************************************** 10081745
[M::ha_hist_line] 18: ************************************************ 9294795
[M::ha_hist_line] 19: ******************************************* 8343261
[M::ha_hist_line] 20: ************************************** 7439039
[M::ha_hist_line] 21: ********************************** 6542366
[M::ha_hist_line] 22: ****************************** 5913583
[M::ha_hist_line] 23: **************************** 5508667
[M::ha_hist_line] 24: *************************** 5255707
[M::ha_hist_line] 25: *************************** 5179877
[M::ha_hist_line] 26: *************************** 5247195
[M::ha_hist_line] 27: **************************** 5448638
[M::ha_hist_line] 28: ***************************** 5692945
[M::ha_hist_line] 29: ******************************* 6008052
[M::ha_hist_line] 30: ******************************** 6277191
[M::ha_hist_line] 31: ********************************** 6553759
[M::ha_hist_line] 32: *********************************** 6720619
[M::ha_hist_line] 33: *********************************** 6876860
[M::ha_hist_line] 34: ************************************ 6997947
[M::ha_hist_line] 35: ************************************* 7110283
[M::ha_hist_line] 36: ************************************* 7195966
[M::ha_hist_line] 37: ************************************* 7212979
[M::ha_hist_line] 38: ************************************* 7289405
[M::ha_hist_line] 39: ************************************** 7427461
[M::ha_hist_line] 40: *************************************** 7663150
[M::ha_hist_line] 41: **************************************** 7851733
[M::ha_hist_line] 42: ****************************************** 8129358
[M::ha_hist_line] 43: ******************************************** 8487293
[M::ha_hist_line] 44: ********************************************* 8832751
[M::ha_hist_line] 45: *********************************************** 9227416
[M::ha_hist_line] 46: ************************************************** 9701100
[M::ha_hist_line] 47: ***************************************************** 10230384
[M::ha_hist_line] 48: ******************************************************* 10792274
[M::ha_hist_line] 49: ********************************************************** 11332228
[M::ha_hist_line] 50: ************************************************************* 11898064
[M::ha_hist_line] 51: **************************************************************** 12517999
[M::ha_hist_line] 52: ******************************************************************** 13164632
[M::ha_hist_line] 53: *********************************************************************** 13875316
[M::ha_hist_line] 54: *************************************************************************** 14613027
[M::ha_hist_line] 55: ******************************************************************************* 15387785
[M::ha_hist_line] 56: *********************************************************************************** 16183132
[M::ha_hist_line] 57: *************************************************************************************** 16856906
[M::ha_hist_line] 58: ******************************************************************************************* 17636197
[M::ha_hist_line] 59: ********************************************************************************************** 18226042
[M::ha_hist_line] 60: ************************************************************************************************ 18646145
[M::ha_hist_line] 61: ************************************************************************************************** 19049769
[M::ha_hist_line] 62: *************************************************************************************************** 19303743
[M::ha_hist_line] 63: **************************************************************************************************** 19432137
[M::ha_hist_line] 64: **************************************************************************************************** 19458901
[M::ha_hist_line] 65: *************************************************************************************************** 19289696
[M::ha_hist_line] 66: ************************************************************************************************* 18929094
[M::ha_hist_line] 67: *********************************************************************************************** 18445537
[M::ha_hist_line] 68: ******************************************************************************************* 17775844
[M::ha_hist_line] 69: *************************************************************************************** 16928012
[M::ha_hist_line] 70: ********************************************************************************** 15983471
[M::ha_hist_line] 71: ***************************************************************************** 14945536
[M::ha_hist_line] 72: ************************************************************************ 13913471
[M::ha_hist_line] 73: ****************************************************************** 12787055
[M::ha_hist_line] 74: ************************************************************ 11685084
[M::ha_hist_line] 75: ****************************************************** 10559582
[M::ha_hist_line] 76: ************************************************* 9514990
[M::ha_hist_line] 77: ******************************************** 8491661
[M::ha_hist_line] 78: *************************************** 7505121
[M::ha_hist_line] 79: ********************************** 6533418
[M::ha_hist_line] 80: ***************************** 5665576
[M::ha_hist_line] 81: ************************* 4908441
[M::ha_hist_line] 82: ********************** 4243839
[M::ha_hist_line] 83: ******************* 3648527
[M::ha_hist_line] 84: **************** 3100641
[M::ha_hist_line] 85: ************** 2637802
[M::ha_hist_line] 86: *********** 2233645
[M::ha_hist_line] 87: ********** 1895222
[M::ha_hist_line] 88: ******** 1629197
[M::ha_hist_line] 89: ******* 1393297
[M::ha_hist_line] 90: ****** 1217140
[M::ha_hist_line] 91: ****** 1071864
[M::ha_hist_line] 92: ***** 951259
[M::ha_hist_line] 93: **** 865946
[M::ha_hist_line] 94: **** 795908
[M::ha_hist_line] 95: **** 743848
[M::ha_hist_line] 96: **** 700633
[M::ha_hist_line] 97: *** 675482
[M::ha_hist_line] 98: *** 650550
[M::ha_hist_line] 99: *** 632107
[M::ha_hist_line] 100: *** 631923
[M::ha_hist_line] 101: *** 630583
[M::ha_hist_line] 102: *** 631134
[M::ha_hist_line] 103: *** 637148
[M::ha_hist_line] 104: *** 638831
[M::ha_hist_line] 105: *** 644870
[M::ha_hist_line] 106: *** 655182

the genomescope result is：

i have no idea about how to adjust it, make it set right peak.

[chhylp123]

What is the peak_hom value reported by Hifiasm?

[MIEFIGH]

The log is:
[M::purge_dups] homozygous read coverage threshold: 124
[M::purge_dups] purge duplication coverage threshold: 155

What is the peak_hom value reported by Hifiasm?

[chhylp123]

It's fine since this value only affects error correction. If Hifiasm is too slow, you might consider setting -N to 3. To ensure a correct assembly, it’s recommended to also set --hom-cov 60.

[sohojiang]

hello, professor,Thank you for such an excellent assembly software.
I have a few questions and look forward to your answers.
my log is :
[M::ha_analyze_count] lowest: count[5] = 7639962
[M::ha_analyze_count] highest: count[29] = 14325660
[M::ha_hist_line] 2: ****************************************************************************************************> 15303348
[M::ha_hist_line] 3: ******************************************************* 7893124
[M::ha_hist_line] 4: *************************************************** 7361479
[M::ha_hist_line] 5: ***************************************************** 7639962
[M::ha_hist_line] 6: ********************************************************* 8212780
[M::ha_hist_line] 7: ************************************************************* 8679195
[M::ha_hist_line] 8: ***************************************************************** 9292734
[M::ha_hist_line] 9: ******************************************************************** 9749907
[M::ha_hist_line] 10: ************************************************************************ 10281644
[M::ha_hist_line] 11: *************************************************************************** 10717308
[M::ha_hist_line] 12: ***************************************************************************** 11074585
[M::ha_hist_line] 13: ******************************************************************************** 11466006
[M::ha_hist_line] 14: ********************************************************************************** 11689881
[M::ha_hist_line] 15: ************************************************************************************ 12094044
[M::ha_hist_line] 16: *************************************************************************************** 12446351
[M::ha_hist_line] 17: **************************************************************************************** 12666461
[M::ha_hist_line] 18: ****************************************************************************************** 12874398
[M::ha_hist_line] 19: ******************************************************************************************* 13090672
[M::ha_hist_line] 20: ********************************************************************************************* 13313944
[M::ha_hist_line] 21: ********************************************************************************************* 13372898
[M::ha_hist_line] 22: *********************************************************************************************** 13634405
[M::ha_hist_line] 23: *********************************************************************************************** 13655899
[M::ha_hist_line] 24: ************************************************************************************************ 13752921
[M::ha_hist_line] 25: ************************************************************************************************* 13884605
[M::ha_hist_line] 26: ************************************************************************************************** 14018680
[M::ha_hist_line] 27: ************************************************************************************************** 14101440
[M::ha_hist_line] 28: **************************************************************************************************** 14262115
[M::ha_hist_line] 29: **************************************************************************************************** 14325660
[M::ha_hist_line] 30: **************************************************************************************************** 14311358
[M::ha_hist_line] 31: **************************************************************************************************** 14274013
[M::ha_hist_line] 32: **************************************************************************************************** 14268465
[M::ha_hist_line] 33: **************************************************************************************************** 14274050
[M::ha_hist_line] 34: **************************************************************************************************** 14279089
[M::ha_hist_line] 35: *************************************************************************************************** 14231399
[M::ha_hist_line] 36: *************************************************************************************************** 14211727
[M::ha_hist_line] 37: *************************************************************************************************** 14160621
[M::ha_hist_line] 38: *************************************************************************************************** 14132638
[M::ha_hist_line] 39: ************************************************************************************************** 14073751
[M::ha_hist_line] 40: ************************************************************************************************** 13990395
[M::ha_hist_line] 41: ************************************************************************************************* 13824612
[M::ha_hist_line] 42: *********************************************************************************************** 13611599
[M::ha_hist_line] 43: ********************************************************************************************** 13433818
[M::ha_hist_line] 44: ******************************************************************************************** 13235460
[M::ha_hist_line] 45: ******************************************************************************************* 12991713
[M::ha_hist_line] 46: ***************************************************************************************** 12769920
[M::ha_hist_line] 47: *************************************************************************************** 12397967
[M::ha_hist_line] 48: ************************************************************************************* 12129829
[M::ha_hist_line] 49: ********************************************************************************** 11765986
[M::ha_hist_line] 50: ******************************************************************************* 11374343
[M::ha_hist_line] 51: ***************************************************************************** 11020394
[M::ha_hist_line] 52: ************************************************************************** 10605306
[M::ha_hist_line] 53: *********************************************************************** 10197092
[M::ha_hist_line] 54: ******************************************************************** 9769375
[M::ha_hist_line] 55: ***************************************************************** 9376885
[M::ha_hist_line] 56: ************************************************************** 8922845
[M::ha_hist_line] 57: *********************************************************** 8443964
[M::ha_hist_line] 58: ******************************************************** 8084788
[M::ha_hist_line] 59: ***************************************************** 7660040
[M::ha_hist_line] 60: *************************************************** 7292074
[M::ha_hist_line] 61: ************************************************ 6918297
[M::ha_hist_line] 62: ********************************************** 6603961
[M::ha_hist_line] 63: ******************************************** 6304091
[M::ha_hist_line] 64: ****************************************** 5994678
[M::ha_hist_line] 65: **************************************** 5713332
[M::ha_hist_line] 66: ************************************** 5482577
[M::ha_hist_line] 67: ************************************* 5271115
[M::ha_hist_line] 68: ************************************ 5105652
[M::ha_hist_line] 69: *********************************** 4943565
[M::ha_hist_line] 70: ********************************** 4824296
[M::ha_hist_line] 71: ********************************* 4745265
[M::ha_hist_line] 72: ********************************* 4677274
[M::ha_hist_line] 73: ******************************** 4638879
[M::ha_hist_line] 74: ******************************** 4589501
[M::ha_hist_line] 75: ******************************** 4592535
[M::ha_hist_line] 76: ******************************** 4611554
[M::ha_hist_line] 77: ******************************** 4600282
[M::ha_hist_line] 78: ******************************** 4608469
[M::ha_hist_line] 79: ******************************** 4653354
[M::ha_hist_line] 80: ******************************** 4633609
[M::ha_hist_line] 81: ********************************* 4663919
[M::ha_hist_line] 82: ********************************* 4697970
[M::ha_hist_line] 83: ********************************* 4693817
[M::ha_hist_line] 84: ********************************* 4687151
[M::ha_hist_line] 85: ********************************* 4734793
[M::ha_hist_line] 86: ********************************* 4765441
[M::ha_hist_line] 87: ********************************** 4803587
[M::ha_hist_line] 88: ********************************** 4821016
[M::ha_hist_line] 89: ********************************** 4833678
[M::ha_hist_line] 90: ********************************** 4875486
[M::ha_hist_line] 91: ********************************** 4877943
[M::ha_hist_line] 92: ********************************** 4829299
[M::ha_hist_line] 93: ********************************* 4795715
[M::ha_hist_line] 94: ********************************* 4745075
[M::ha_hist_line] 95: ********************************* 4706215
[M::ha_hist_line] 96: ********************************* 4665823
[M::ha_hist_line] 97: ******************************** 4626927
[M::ha_hist_line] 98: ******************************** 4612081
[M::ha_hist_line] 99: ******************************** 4622559
[M::ha_hist_line] 100: ******************************** 4569587
[M::ha_hist_line] 101: ******************************* 4503832
[M::ha_hist_line] 102: ******************************* 4461185
[M::ha_hist_line] 103: ******************************* 4395687
[M::ha_hist_line] 104: ****************************** 4328820
[M::ha_hist_line] 105: ****************************** 4269607
[M::ha_hist_line] 106: ***************************** 4183284
[M::ha_hist_line] 107: **************************** 4081493
[M::ha_hist_line] 108: **************************** 3998726
[M::ha_hist_line] 109: *************************** 3872116
[M::ha_hist_line] 110: ************************** 3760267
[M::ha_hist_line] 111: ************************** 3655192
[M::ha_hist_line] 112: ************************ 3501095
[M::ha_hist_line] 113: ************************ 3382500
[M::ha_hist_line] 114: *********************** 3253731
[M::ha_hist_line] 115: ********************** 3085145
[M::ha_hist_line] 116: ******************** 2930122
[M::ha_hist_line] 117: ******************* 2756504
[M::ha_hist_line] 118: ****************** 2616350
[M::ha_hist_line] 119: ***************** 2470621
[M::ha_hist_line] 120: **************** 2320567
[M::ha_hist_line] 121: *************** 2163923
[M::ha_hist_line] 122: ************** 2032147
[M::ha_hist_line] 123: ************* 1894797
[M::ha_hist_line] 124: ************ 1766082
[M::ha_hist_line] 125: *********** 1627026
[M::ha_hist_line] 126: ********** 1480435
[M::ha_hist_line] 127: ********* 1347109
[M::ha_hist_line] 128: ********* 1237230
[M::ha_hist_line] 129: ******** 1141424
[M::ha_hist_line] 130: ******* 1043244
[M::ha_hist_line] 131: ******* 952041
[M::ha_hist_line] 132: ****** 866922
[M::ha_hist_line] 133: ***** 785508
[M::ha_hist_line] 134: ***** 702653
[M::ha_hist_line] 135: **** 633889
[M::ha_hist_line] 136: **** 572306
[M::ha_hist_line] 137: **** 501902
[M::ha_hist_line] 138: *** 453807

and the peak_hom is:
[M::purge_dups] homozygous read coverage threshold: 97
[M::purge_dups] purge duplication coverage threshold: 122

As shown above, the first peak represents the heterozygous peak, and the second peak represents the homozygous peak. Theoretically, the value of the homozygous peak should be higher than that of the heterozygous peak, as indicated by the survey results.

So, should I adjust the hom-cov to 14325660 ( hom peak), or to 29 (hom cov)?

Looking forward to your reply. Wishing you a pleasant life!