Changing homozygous and heterozygous peak values

[chklopp]

hifiasm 0.15.1 does not correctly find the peak_hom and peak_het values in the example hereunder (see kmer histogram).
[M::ha_pt_gen] peak_hom: 19; peak_het: -1

From my point of view :
peak_hom = 40
peak_het = 19

How could I give these values to hifiasm?

[M::ha_assemble::37423.850[email protected]] ==> corrected reads for round 3
[M::ha_assemble] # bases: 150902074695; # corrected bases: 2111072; # recorrected bases: 150296
[M::ha_assemble] size of buffer: 10.600GB
[M::ha_pt_gen::37855.26741.41] ==> counted 124164072 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[5] = 634393
[M::ha_analyze_count] highest: count[19] = 4209179
[M::ha_hist_line] 1: *************************************************************************************** 3680656
[M::ha_hist_line] 2: ************** 580457
[M::ha_hist_line] 3: *********** 463191
[M::ha_hist_line] 4: ************* 542363
[M::ha_hist_line] 5: *************** 634393
[M::ha_hist_line] 6: ****************** 744747
[M::ha_hist_line] 7: ********************* 891406
[M::ha_hist_line] 8: ************************* 1059281
[M::ha_hist_line] 9: ****************************** 1280454
[M::ha_hist_line] 10: ************************************ 1524384
[M::ha_hist_line] 11: ******************************************* 1816116
[M::ha_hist_line] 12: *************************************************** 2152244
[M::ha_hist_line] 13: ************************************************************ 2508279
[M::ha_hist_line] 14: ********************************************************************* 2909529
[M::ha_hist_line] 15: ****************************************************************************** 3286670
[M::ha_hist_line] 16: ************************************************************************************** 3637683
[M::ha_hist_line] 17: ********************************************************************************************* 3914204
[M::ha_hist_line] 18: ************************************************************************************************** 4114438
[M::ha_hist_line] 19: **************************************************************************************************** 4209179
[M::ha_hist_line] 20: **************************************************************************************************** 4208508
[M::ha_hist_line] 21: ************************************************************************************************** 4106595
[M::ha_hist_line] 22: ********************************************************************************************* 3904024
[M::ha_hist_line] 23: *************************************************************************************** 3643017
[M::ha_hist_line] 24: ******************************************************************************* 3346051
[M::ha_hist_line] 25: *********************************************************************** 3005507
[M::ha_hist_line] 26: *************************************************************** 2669868
[M::ha_hist_line] 27: ******************************************************** 2360101
[M::ha_hist_line] 28: ************************************************** 2085162
[M::ha_hist_line] 29: ******************************************** 1854049
[M::ha_hist_line] 30: **************************************** 1667191
[M::ha_hist_line] 31: ************************************ 1529083
[M::ha_hist_line] 32: ********************************** 1439421
[M::ha_hist_line] 33: ********************************* 1373079
[M::ha_hist_line] 34: ******************************** 1350904
[M::ha_hist_line] 35: ******************************** 1330535
[M::ha_hist_line] 36: ******************************** 1342521
[M::ha_hist_line] 37: ******************************** 1347679
[M::ha_hist_line] 38: ******************************** 1363680
[M::ha_hist_line] 39: ********************************* 1373288
[M::ha_hist_line] 40: ********************************* 1386239
[M::ha_hist_line] 41: ********************************* 1378370
[M::ha_hist_line] 42: ********************************* 1368569
[M::ha_hist_line] 43: ******************************** 1342774
[M::ha_hist_line] 44: ******************************* 1322570
[M::ha_hist_line] 45: ******************************* 1287658
[M::ha_hist_line] 46: ****************************** 1248241
[M::ha_hist_line] 47: ***************************** 1202372
[M::ha_hist_line] 48: *************************** 1156425
[M::ha_hist_line] 49: ************************** 1106569
[M::ha_hist_line] 50: ************************* 1058136
[M::ha_hist_line] 51: ************************ 1005292
[M::ha_hist_line] 52: *********************** 956906
[M::ha_hist_line] 53: ********************** 910194
[M::ha_hist_line] 54: ********************* 868824
[M::ha_hist_line] 55: ******************** 826746
[M::ha_hist_line] 56: ******************* 794039
[M::ha_hist_line] 57: ****************** 763301
[M::ha_hist_line] 58: ****************** 738984
[M::ha_hist_line] 59: ***************** 713103
[M::ha_hist_line] 60: ***************** 695685
[M::ha_hist_line] 61: **************** 677258
[M::ha_hist_line] 62: **************** 660077
[M::ha_hist_line] 63: *************** 647566
[M::ha_hist_line] 64: *************** 636289
[M::ha_hist_line] 65: *************** 627069
[M::ha_hist_line] 66: *************** 611445
[M::ha_hist_line] 67: ************** 601242
[M::ha_hist_line] 68: ************** 594293
[M::ha_hist_line] 69: ************** 585238
[M::ha_hist_line] 70: ************** 575025
[M::ha_hist_line] 71: ************* 566723
[M::ha_hist_line] 72: ************* 555780
[M::ha_hist_line] 73: ************* 546730
[M::ha_hist_line] 74: ************* 537520
[M::ha_hist_line] 75: ************ 526034
[M::ha_hist_line] 76: ************ 512341
[M::ha_hist_line] 77: ************ 496539
[M::ha_hist_line] 78: ************ 484328
[M::ha_hist_line] 79: *********** 472230
[M::ha_hist_line] 80: *********** 456503
[M::ha_hist_line] 81: ********** 440535
[M::ha_hist_line] 82: ********** 425369
[M::ha_hist_line] 83: ********** 406948
[M::ha_hist_line] 84: ********* 393958
[M::ha_hist_line] 85: ********* 378328
[M::ha_hist_line] 86: ********* 362340
[M::ha_hist_line] 87: ******** 347333
[M::ha_hist_line] 88: ******** 334557
[M::ha_hist_line] 89: ******** 319161
[M::ha_hist_line] 90: ******* 307085
[M::ha_hist_line] 91: ******* 294138
[M::ha_hist_line] 92: ******* 280701
[M::ha_hist_line] 93: ****** 269732
[M::ha_hist_line] 94: ****** 258954
[M::ha_hist_line] 95: ***** 227552
[M::ha_hist_line] 96: **** 171776
[M::ha_hist_line] 97: ** 102470
[M::ha_hist_line] 98: * 51429
[M::ha_hist_line] 99: * 22639
[M::ha_hist_line] rest: 17903
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 19; peak_het: -1
[M::ha_pt_gen::38354.51441.30] ==> indexed 4072927351 positions
[M::ha_assemble::40455.523[email protected]] ==> found overlaps for the final round

[chhylp123]

You can manually set hom peak by '--purge-cov'. By the way, could you please show the following number in the log file? It is the real peak used for phasing.

[M::purge_dups] purge duplication coverage threshold:

And could you also show the following number if you are using Hi-C?

[M::stat] # heterozygous bases: 6179497799; # homozygous bases: 480824972

[chklopp]

[M::purge_dups] purge duplication coverage threshold: 47

[M::stat] # heterozygous bases: 7926240829; # homozygous bases: 156123352

[chhylp123]

Since 47 is a little bit larger than 42 (hom k-mer peak), I guess hfiiasm already found the right peak. Is there something wrong for the assemblies?