Is such a k-mer plot normal?

[YanCheer]

As exmplified in Issue10 and Issue49, a good k-mer plot for heterozygous samples should have two peaks of which the smaller one is around the heterozygous read coverage and the larger around the homozygous. And the smaller peaks are HIGHER than the larger as in the above two good examples.

My k-mer plot also shows two peaks, but the smaller peak is LOWER than the larger. I wonder if this implied some sort of errors or warnings in my original data or the special case of my sample?

[M::ha_analyze_count] lowest: count[6] = 2125610 [M::ha_analyze_count] highest: count[47] = 27712519 [M::ha_hist_line] 2: ******************** 5453856 [M::ha_hist_line] 3: ********* 2600588 [M::ha_hist_line] 4: ******** 2298149 [M::ha_hist_line] 5: ******** 2146925 [M::ha_hist_line] 6: ******** 2125610 [M::ha_hist_line] 7: ******** 2192293 [M::ha_hist_line] 8: ********* 2424623 [M::ha_hist_line] 9: ********** 2702840 [M::ha_hist_line] 10: *********** 3122281 [M::ha_hist_line] 11: ************* 3660448 [M::ha_hist_line] 12: **************** 4469464 [M::ha_hist_line] 13: ******************** 5472872 [M::ha_hist_line] 14: ************************ 6680176 [M::ha_hist_line] 15: ****************************** 8305315 [M::ha_hist_line] 16: ************************************ 10049299 [M::ha_hist_line] 17: ******************************************* 11928773 [M::ha_hist_line] 18: ************************************************** 13939095 [M::ha_hist_line] 19: ********************************************************* 15725702 [M::ha_hist_line] 20: *************************************************************** 17448468 [M::ha_hist_line] 21: ******************************************************************* 18649639 [M::ha_hist_line] 22: ********************************************************************** 19445261 [M::ha_hist_line] 23: ************************************************************************ 19928678 [M::ha_hist_line] 24: *********************************************************************** 19778630 [M::ha_hist_line] 25: ********************************************************************* 19162189 [M::ha_hist_line] 26: ****************************************************************** 18155434 [M::ha_hist_line] 27: ************************************************************** 17106676 [M::ha_hist_line] 28: ********************************************************* 15787893 [M::ha_hist_line] 29: **************************************************** 14536096 [M::ha_hist_line] 30: ************************************************* 13543114 [M::ha_hist_line] 31: ********************************************** 12833846 [M::ha_hist_line] 32: ********************************************* 12383060 [M::ha_hist_line] 33: ******************************************** 12307665 [M::ha_hist_line] 34: ********************************************** 12692762 [M::ha_hist_line] 35: ************************************************ 13412706 [M::ha_hist_line] 36: **************************************************** 14403120 [M::ha_hist_line] 37: ********************************************************* 15678271 [M::ha_hist_line] 38: ************************************************************** 17147659 [M::ha_hist_line] 39: ******************************************************************** 18748237 [M::ha_hist_line] 40: ************************************************************************** 20384351 [M::ha_hist_line] 41: ******************************************************************************* 21998624 [M::ha_hist_line] 42: ************************************************************************************* 23604249 [M::ha_hist_line] 43: ****************************************************************************************** 25038333 [M::ha_hist_line] 44: *********************************************************************************************** 26265158 [M::ha_hist_line] 45: ************************************************************************************************** 27027200 [M::ha_hist_line] 46: **************************************************************************************************** 27581400 [M::ha_hist_line] 47: **************************************************************************************************** 27712519 [M::ha_hist_line] 48: *************************************************************************************************** 27472275 [M::ha_hist_line] 49: ************************************************************************************************* 26871390 [M::ha_hist_line] 50: ********************************************************************************************** 26100679 [M::ha_hist_line] 51: ***************************************************************************************** 24787360 [M::ha_hist_line] 52: *********************************************************************************** 23086431 [M::ha_hist_line] 53: ***************************************************************************** 21261823 [M::ha_hist_line] 54: ********************************************************************** 19414101 [M::ha_hist_line] 55: *************************************************************** 17332103 [M::ha_hist_line] 56: ******************************************************* 15303278 [M::ha_hist_line] 57: ************************************************ 13391423 [M::ha_hist_line] 58: ***************************************** 11495486 [M::ha_hist_line] 59: *********************************** 9809959 [M::ha_hist_line] 60: ****************************** 8287287 [M::ha_hist_line] 61: ************************* 6913725 [M::ha_hist_line] 62: ******************** 5677361 [M::ha_hist_line] 63: ***************** 4696075 [M::ha_hist_line] 64: ************** 3753339 [M::ha_hist_line] 65: *********** 3008953 [M::ha_hist_line] 66: ********* 2371004 [M::ha_hist_line] 67: ******* 1866927 [M::ha_hist_line] 68: ***** 1451842 [M::ha_hist_line] 69: **** 1136616 [M::ha_hist_line] 70: *** 866428 [M::ha_hist_line] 71: ** 649436 [M::ha_hist_line] 72: ** 508225 [M::ha_hist_line] 73: * 414301 [M::ha_hist_line] 74: * 333182 [M::ha_hist_line] 75: * 271241 [M::ha_hist_line] 76: * 223738 [M::ha_hist_line] 77: * 188763 [M::ha_hist_line] 78: * 163899 [M::ha_hist_line] 79: * 146305 [M::ha_hist_line] rest: ************************* 7012300 [M::ha_analyze_count] left: count[23] = 19928678 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::1626.44813.41] ==> counted 1976416 distinct minimizer k-mers [M::ha_ft_gen::1630.568[email protected]] ==> filtered out 1976416 k-mers occurring 235 or more times [M::ha_opt_update_cov] updated max_n_chain to 235 [M::yak_count] collected 1463544421 minimizers [M::ha_pt_gen::2235.471*13.21] ==> counted 55746676 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 130163 [M::ha_analyze_count] highest: count[47] = 1068344 [M::ha_hist_line] 1: **************************************************************************************> 17590237 [M::ha_hist_line] 2: ********************************************** 488757 [M::ha_hist_line] 3: ***************** 185485 [M::ha_hist_line] 4: ************** 146999 [M::ha_hist_line] 5: ************* 133769 [M::ha_hist_line] 6: ************ 130163 [M::ha_hist_line] 7: ************ 132424 [M::ha_hist_line] 8: ************* 142810 [M::ha_hist_line] 9: *************** 155736 [M::ha_hist_line] 10: **************** 174729 [M::ha_hist_line] 11: ******************* 198893 [M::ha_hist_line] 12: ********************** 233747 [M::ha_hist_line] 13: ************************** 278861 [M::ha_hist_line] 14: ******************************* 332935 [M::ha_hist_line] 15: ************************************** 402040 [M::ha_hist_line] 16: ********************************************* 478270 [M::ha_hist_line] 17: **************************************************** 557802 [M::ha_hist_line] 18: ************************************************************ 643177 [M::ha_hist_line] 19: ******************************************************************* 715900 [M::ha_hist_line] 20: ************************************************************************** 786085 [M::ha_hist_line] 21: ****************************************************************************** 832833 [M::ha_hist_line] 22: ********************************************************************************* 861256 [M::ha_hist_line] 23: ********************************************************************************** 877606 [M::ha_hist_line] 24: ********************************************************************************* 865461 [M::ha_hist_line] 25: ****************************************************************************** 832760 [M::ha_hist_line] 26: ************************************************************************** 786363 [M::ha_hist_line] 27: ********************************************************************* 734688 [M::ha_hist_line] 28: *************************************************************** 676276 [M::ha_hist_line] 29: ********************************************************** 619602 [M::ha_hist_line] 30: ****************************************************** 574259 [M::ha_hist_line] 31: *************************************************** 540310 [M::ha_hist_line] 32: ************************************************ 516735 [M::ha_hist_line] 33: ************************************************ 511011 [M::ha_hist_line] 34: ************************************************* 522482 [M::ha_hist_line] 35: *************************************************** 546378 [M::ha_hist_line] 36: ****************************************************** 581509 [M::ha_hist_line] 37: *********************************************************** 628364 [M::ha_hist_line] 38: **************************************************************** 683899 [M::ha_hist_line] 39: ********************************************************************** 745376 [M::ha_hist_line] 40: *************************************************************************** 806075 [M::ha_hist_line] 41: ********************************************************************************* 865272 [M::ha_hist_line] 42: *************************************************************************************** 925841 [M::ha_hist_line] 43: ******************************************************************************************** 977733 [M::ha_hist_line] 44: ************************************************************************************************ 1021154 [M::ha_hist_line] 45: ************************************************************************************************** 1047960 [M::ha_hist_line] 46: **************************************************************************************************** 1066546 [M::ha_hist_line] 47: **************************************************************************************************** 1068344 [M::ha_hist_line] 48: *************************************************************************************************** 1054158 [M::ha_hist_line] 49: ************************************************************************************************ 1029367 [M::ha_hist_line] 50: ********************************************************************************************* 994303 [M::ha_hist_line] 51: **************************************************************************************** 941602 [M::ha_hist_line] 52: ********************************************************************************** 875424 [M::ha_hist_line] 53: *************************************************************************** 803692 [M::ha_hist_line] 54: ******************************************************************** 731420 [M::ha_hist_line] 55: ************************************************************* 652223 [M::ha_hist_line] 56: ****************************************************** 574588 [M::ha_hist_line] 57: *********************************************** 503016 [M::ha_hist_line] 58: **************************************** 430163 [M::ha_hist_line] 59: *********************************** 368680 [M::ha_hist_line] 60: ***************************** 310516 [M::ha_hist_line] 61: ************************ 259516 [M::ha_hist_line] 62: ******************** 214562 [M::ha_hist_line] 63: ***************** 177251 [M::ha_hist_line] 64: ************* 143042 [M::ha_hist_line] 65: *********** 115631 [M::ha_hist_line] 66: ********* 92354 [M::ha_hist_line] 67: ******* 73796 [M::ha_hist_line] 68: ****** 59021 [M::ha_hist_line] 69: **** 47314 [M::ha_hist_line] 70: *** 37247 [M::ha_hist_line] 71: *** 29299 [M::ha_hist_line] 72: ** 24169 [M::ha_hist_line] 73: ** 20804 [M::ha_hist_line] 74: ** 17786 [M::ha_hist_line] 75: * 15243 [M::ha_hist_line] 76: * 13384 [M::ha_hist_line] 77: * 12028 [M::ha_hist_line] 78: * 11226 [M::ha_hist_line] 79: * 10377 [M::ha_hist_line] 80: * 9690 [M::ha_hist_line] 81: * 9144 [M::ha_hist_line] 82: * 8672 [M::ha_hist_line] 83: * 8376 [M::ha_hist_line] 84: * 7984 [M::ha_hist_line] 85: * 7873 [M::ha_hist_line] 86: * 7545 [M::ha_hist_line] 87: * 7739 [M::ha_hist_line] 88: * 7420 [M::ha_hist_line] 89: * 7320 [M::ha_hist_line] 90: * 7195 [M::ha_hist_line] 91: * 7103 [M::ha_hist_line] 92: * 7207 [M::ha_hist_line] 93: * 6946 [M::ha_hist_line] 94: * 6865 [M::ha_hist_line] 95: * 6731 [M::ha_hist_line] 96: * 6475 [M::ha_hist_line] 97: * 6318 [M::ha_hist_line] 98: * 6249 [M::ha_hist_line] 99: * 6315 [M::ha_hist_line] 100: * 6173 [M::ha_hist_line] 101: * 5782 [M::ha_hist_line] 102: * 5714 [M::ha_hist_line] 103: * 5727 [M::ha_hist_line] 104: * 5428 [M::ha_hist_line] 105: * 5442 [M::ha_hist_line] rest: **************************** 295129 [M::ha_analyze_count] left: count[23] = 877606 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::2235.59113.22] ==> counted 38156439 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1463544421 minimizers [M::ha_pt_gen::2465.69114.68] ==> indexed 1445954184 positions, counted 38156439 distinct minimizer k-mers sh 00.Scripts/02.AlltheCells.hifias[M::ha_assemble::4791.521[email protected]] ==> corrected reads for round 1 [M::ha_assemble] # bases: 54190381756; # corrected bases: 82102298; # recorrected bases: 85786 [M::ha_assemble] size of buffer: 12.223GB [M::yak_count] collected 1462371695 minimizers [M::ha_pt_gen::4933.97640.45] ==> counted 38571258 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 123680 [M::ha_analyze_count] highest: count[47] = 1062125 [M::ha_hist_line] 1: ******************************************************************************* 839947 [M::ha_hist_line] 2: ************** 153744 [M::ha_hist_line] 3: ************ 130830 [M::ha_hist_line] 4: ************ 129587 [M::ha_hist_line] 5: ************ 124947 [M::ha_hist_line] 6: ************ 123680 [M::ha_hist_line] 7: ************ 127440 [M::ha_hist_line] 8: ************* 137878 [M::ha_hist_line] 9: ************** 149773 [M::ha_hist_line] 10: **************** 168779 [M::ha_hist_line] 11: ****************** 189920 [M::ha_hist_line] 12: ********************* 224683 [M::ha_hist_line] 13: ************************* 266712 [M::ha_hist_line] 14: ****************************** 316186 [M::ha_hist_line] 15: ************************************ 384657 [M::ha_hist_line] 16: ******************************************* 455486 [M::ha_hist_line] 17: ************************************************** 533795 [M::ha_hist_line] 18: ********************************************************** 618721 [M::ha_hist_line] 19: ***************************************************************** 692610 [M::ha_hist_line] 20: ************************************************************************ 764093 [M::ha_hist_line] 21: ***************************************************************************** 812885 [M::ha_hist_line] 22: ******************************************************************************** 848002 [M::ha_hist_line] 23: ********************************************************************************** 869487 [M::ha_hist_line] 24: ********************************************************************************* 864611 [M::ha_hist_line] 25: ******************************************************************************* 836815 [M::ha_hist_line] 26: *************************************************************************** 793494 [M::ha_hist_line] 27: ********************************************************************** 745041 [M::ha_hist_line] 28: ***************************************************************** 686108 [M::ha_hist_line] 29: *********************************************************** 628782 [M::ha_hist_line] 30: ******************************************************* 578946 [M::ha_hist_line] 31: *************************************************** 544256 [M::ha_hist_line] 32: ************************************************ 513905 [M::ha_hist_line] 33: *********************************************** 501327 [M::ha_hist_line] 34: ************************************************ 507579 [M::ha_hist_line] 35: ************************************************** 525956 [M::ha_hist_line] 36: **************************************************** 557081 [M::ha_hist_line] 37: ********************************************************* 600158 [M::ha_hist_line] 38: ************************************************************* 650312 [M::ha_hist_line] 39: ******************************************************************* 710233 [M::ha_hist_line] 40: ************************************************************************ 766249 [M::ha_hist_line] 41: ****************************************************************************** 828821 [M::ha_hist_line] 42: ************************************************************************************ 891061 [M::ha_hist_line] 43: ***************************************************************************************** 944576 [M::ha_hist_line] 44: ********************************************************************************************* 992679 [M::ha_hist_line] 45: ************************************************************************************************* 1025881 [M::ha_hist_line] 46: *************************************************************************************************** 1049236 [M::ha_hist_line] 47: **************************************************************************************************** 1062125 [M::ha_hist_line] 48: *************************************************************************************************** 1056117 [M::ha_hist_line] 49: ************************************************************************************************** 1036021 [M::ha_hist_line] 50: *********************************************************************************************** 1012437 [M::ha_hist_line] 51: ******************************************************************************************* 969486 [M::ha_hist_line] 52: ************************************************************************************* 905024 [M::ha_hist_line] 53: ******************************************************************************* 839514 [M::ha_hist_line] 54: ************************************************************************ 768075 [M::ha_hist_line] 55: ****************************************************************** 696862 [M::ha_hist_line] 56: ********************************************************** 616218 [M::ha_hist_line] 57: *************************************************** 543995 [M::ha_hist_line] 58: ******************************************** 469749 [M::ha_hist_line] 59: ************************************** 403234 [M::ha_hist_line] 60: ******************************** 343699 [M::ha_hist_line] 61: *************************** 288974 [M::ha_hist_line] 62: *********************** 240442 [M::ha_hist_line] 63: ******************* 199772 [M::ha_hist_line] 64: *************** 162928 [M::ha_hist_line] 65: ************* 133472 [M::ha_hist_line] 66: ********** 105987 [M::ha_hist_line] 67: ******** 85208 [M::ha_hist_line] 68: ****** 67834 [M::ha_hist_line] 69: ***** 54779 [M::ha_hist_line] 70: **** 44234 [M::ha_hist_line] 71: *** 33906 [M::ha_hist_line] 72: *** 27296 [M::ha_hist_line] 73: ** 23431 [M::ha_hist_line] 74: ** 19369 [M::ha_hist_line] 75: ** 16953 [M::ha_hist_line] 76: * 14641 [M::ha_hist_line] 77: * 12842 [M::ha_hist_line] 78: * 11722 [M::ha_hist_line] 79: * 10753 [M::ha_hist_line] 80: * 10213 [M::ha_hist_line] 81: * 9484 [M::ha_hist_line] 82: * 9024 [M::ha_hist_line] 83: * 8467 [M::ha_hist_line] 84: * 8210 [M::ha_hist_line] 85: * 7629 [M::ha_hist_line] 86: * 7745 [M::ha_hist_line] 87: * 7571 [M::ha_hist_line] 88: * 7457 [M::ha_hist_line] 89: * 7456 [M::ha_hist_line] 90: * 7226 [M::ha_hist_line] 91: * 7129 [M::ha_hist_line] 92: * 6951 [M::ha_hist_line] 93: * 7033 [M::ha_hist_line] 94: * 7024 [M::ha_hist_line] 95: * 6903 [M::ha_hist_line] 96: * 6684 [M::ha_hist_line] 97: * 6374 [M::ha_hist_line] 98: * 6316 [M::ha_hist_line] 99: * 6225 [M::ha_hist_line] 100: * 6254 [M::ha_hist_line] 101: * 6029 [M::ha_hist_line] 102: * 5751 [M::ha_hist_line] 103: * 5706 [M::ha_hist_line] 104: * 5471 [M::ha_hist_line] 105: * 5582 [M::ha_hist_line] 106: * 5446 [M::ha_hist_line] rest: **************************** 295850 [M::ha_analyze_count] left: count[23] = 869487 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::4934.07240.45] ==> counted 37731311 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1462371695 minimizers [M::ha_pt_gen::5147.50839.91] ==> indexed 1461531748 positions, counted 37731311 distinct minimizer k-mers [M::ha_assemble::6602.220[email protected]] ==> corrected reads for round 2 [M::ha_assemble] # bases: 54188266870; # corrected bases: 2145610; # recorrected bases: 57622 [M::ha_assemble] size of buffer: 11.699GB [M::yak_count] collected 1462319994 minimizers [M::ha_pt_gen::6737.66850.64] ==> counted 38171003 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 123687 [M::ha_analyze_count] highest: count[47] = 1061577 [M::ha_hist_line] 1: ****************************************** 446705 [M::ha_hist_line] 2: ************** 148886 [M::ha_hist_line] 3: ************ 129399 [M::ha_hist_line] 4: ************ 129521 [M::ha_hist_line] 5: ************ 124203 [M::ha_hist_line] 6: ************ 123687 [M::ha_hist_line] 7: ************ 127318 [M::ha_hist_line] 8: ************* 137744 [M::ha_hist_line] 9: ************** 149436 [M::ha_hist_line] 10: **************** 168744 [M::ha_hist_line] 11: ****************** 189971 [M::ha_hist_line] 12: ********************* 224159 [M::ha_hist_line] 13: ************************* 266639 [M::ha_hist_line] 14: ****************************** 315698 [M::ha_hist_line] 15: ************************************ 384206 [M::ha_hist_line] 16: ******************************************* 454972 [M::ha_hist_line] 17: ************************************************** 533226 [M::ha_hist_line] 18: ********************************************************** 618080 [M::ha_hist_line] 19: ***************************************************************** 691965 [M::ha_hist_line] 20: ************************************************************************ 763781 [M::ha_hist_line] 21: ***************************************************************************** 812482 [M::ha_hist_line] 22: ******************************************************************************** 847998 [M::ha_hist_line] 23: ********************************************************************************** 869303 [M::ha_hist_line] 24: ********************************************************************************* 864672 [M::ha_hist_line] 25: ******************************************************************************* 836825 [M::ha_hist_line] 26: *************************************************************************** 793776 [M::ha_hist_line] 27: ********************************************************************** 745449 [M::ha_hist_line] 28: ***************************************************************** 686452 [M::ha_hist_line] 29: *********************************************************** 628655 [M::ha_hist_line] 30: ******************************************************* 578860 [M::ha_hist_line] 31: *************************************************** 544567 [M::ha_hist_line] 32: ************************************************ 514015 [M::ha_hist_line] 33: *********************************************** 501360 [M::ha_hist_line] 34: ************************************************ 507268 [M::ha_hist_line] 35: ************************************************** 525685 [M::ha_hist_line] 36: **************************************************** 556742 [M::ha_hist_line] 37: ******************************************************** 599702 [M::ha_hist_line] 38: ************************************************************* 649827 [M::ha_hist_line] 39: ******************************************************************* 709695 [M::ha_hist_line] 40: ************************************************************************ 765739 [M::ha_hist_line] 41: ****************************************************************************** 827653 [M::ha_hist_line] 42: ************************************************************************************ 890527 [M::ha_hist_line] 43: ***************************************************************************************** 943964 [M::ha_hist_line] 44: ********************************************************************************************* 991797 [M::ha_hist_line] 45: ************************************************************************************************* 1025844 [M::ha_hist_line] 46: *************************************************************************************************** 1048792 [M::ha_hist_line] 47: **************************************************************************************************** 1061577 [M::ha_hist_line] 48: *************************************************************************************************** 1056241 [M::ha_hist_line] 49: ************************************************************************************************** 1036201 [M::ha_hist_line] 50: *********************************************************************************************** 1012640 [M::ha_hist_line] 51: ******************************************************************************************* 970207 [M::ha_hist_line] 52: ************************************************************************************* 905541 [M::ha_hist_line] 53: ******************************************************************************* 839733 [M::ha_hist_line] 54: ************************************************************************ 768706 [M::ha_hist_line] 55: ****************************************************************** 697564 [M::ha_hist_line] 56: ********************************************************** 617143 [M::ha_hist_line] 57: *************************************************** 544693 [M::ha_hist_line] 58: ******************************************** 470422 [M::ha_hist_line] 59: ************************************** 403949 [M::ha_hist_line] 60: ******************************** 344414 [M::ha_hist_line] 61: *************************** 289573 [M::ha_hist_line] 62: *********************** 241099 [M::ha_hist_line] 63: ******************* 200063 [M::ha_hist_line] 64: *************** 163401 [M::ha_hist_line] 65: ************* 133952 [M::ha_hist_line] 66: ********** 106357 [M::ha_hist_line] 67: ******** 85372 [M::ha_hist_line] 68: ****** 68114 [M::ha_hist_line] 69: ***** 54960 [M::ha_hist_line] 70: **** 44387 [M::ha_hist_line] 71: *** 34012 [M::ha_hist_line] 72: *** 27417 [M::ha_hist_line] 73: ** 23422 [M::ha_hist_line] 74: ** 19479 [M::ha_hist_line] 75: ** 16947 [M::ha_hist_line] 76: * 14533 [M::ha_hist_line] 77: * 12871 [M::ha_hist_line] 78: * 11674 [M::ha_hist_line] 79: * 10727 [M::ha_hist_line] 80: * 10224 [M::ha_hist_line] 81: * 9643 [M::ha_hist_line] 82: * 9014 [M::ha_hist_line] 83: * 8517 [M::ha_hist_line] 84: * 8104 [M::ha_hist_line] 85: * 7679 [M::ha_hist_line] 86: * 7796 [M::ha_hist_line] 87: * 7593 [M::ha_hist_line] 88: * 7410 [M::ha_hist_line] 89: * 7536 [M::ha_hist_line] 90: * 7174 [M::ha_hist_line] 91: * 7109 [M::ha_hist_line] 92: * 7053 [M::ha_hist_line] 93: * 7050 [M::ha_hist_line] 94: * 6966 [M::ha_hist_line] 95: * 6823 [M::ha_hist_line] 96: * 6680 [M::ha_hist_line] 97: * 6412 [M::ha_hist_line] 98: * 6303 [M::ha_hist_line] 99: * 6218 [M::ha_hist_line] 100: * 6252 [M::ha_hist_line] 101: * 6039 [M::ha_hist_line] 102: * 5721 [M::ha_hist_line] 103: * 5742 [M::ha_hist_line] 104: * 5446 [M::ha_hist_line] 105: * 5584 [M::ha_hist_line] 106: * 5486 [M::ha_hist_line] rest: **************************** 296049 [M::ha_analyze_count] left: count[23] = 869303 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::6737.88250.64] ==> counted 37724298 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1462319994 minimizers [M::ha_pt_gen::6954.21249.97] ==> indexed 1461873289 positions, counted 37724298 distinct minimizer k-mers [M::ha_assemble::9507.724[email protected]] ==> corrected reads for round 3 [M::ha_assemble] # bases: 54188096343; # corrected bases: 261434; # recorrected bases: 57838 [M::ha_assemble] size of buffer: 11.726GB [M::yak_count] collected 1462314501 minimizers [M::ha_pt_gen::9660.53551.26] ==> counted 38150566 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 123617 [M::ha_analyze_count] highest: count[47] = 1061516 [M::ha_hist_line] 1: **************************************** 427720 [M::ha_hist_line] 2: ************** 148021 [M::ha_hist_line] 3: ************ 129152 [M::ha_hist_line] 4: ************ 129352 [M::ha_hist_line] 5: ************ 124126 [M::ha_hist_line] 6: ************ 123617 [M::ha_hist_line] 7: ************ 127367 [M::ha_hist_line] 8: ************* 137661 [M::ha_hist_line] 9: ************** 149406 [M::ha_hist_line] 10: **************** 168773 [M::ha_hist_line] 11: ****************** 189912 [M::ha_hist_line] 12: ********************* 224241 [M::ha_hist_line] 13: ************************* 266565 [M::ha_hist_line] 14: ****************************** 315598 [M::ha_hist_line] 15: ************************************ 384237 [M::ha_hist_line] 16: ******************************************* 454923 [M::ha_hist_line] 17: ************************************************** 533310 [M::ha_hist_line] 18: ********************************************************** 617980 [M::ha_hist_line] 19: ***************************************************************** 691940 [M::ha_hist_line] 20: ************************************************************************ 763722 [M::ha_hist_line] 21: ***************************************************************************** 812448 [M::ha_hist_line] 22: ******************************************************************************** 848047 [M::ha_hist_line] 23: ********************************************************************************** 869322 [M::ha_hist_line] 24: ********************************************************************************* 864632 [M::ha_hist_line] 25: ******************************************************************************* 836877 [M::ha_hist_line] 26: *************************************************************************** 793784 [M::ha_hist_line] 27: ********************************************************************** 745397 [M::ha_hist_line] 28: ***************************************************************** 686446 [M::ha_hist_line] 29: *********************************************************** 628702 [M::ha_hist_line] 30: ******************************************************* 578853 [M::ha_hist_line] 31: *************************************************** 544556 [M::ha_hist_line] 32: ************************************************ 514014 [M::ha_hist_line] 33: *********************************************** 501327 [M::ha_hist_line] 34: ************************************************ 507392 [M::ha_hist_line] 35: ************************************************** 525601 [M::ha_hist_line] 36: **************************************************** 556787 [M::ha_hist_line] 37: ******************************************************** 599694 [M::ha_hist_line] 38: ************************************************************* 649774 [M::ha_hist_line] 39: ******************************************************************* 709638 [M::ha_hist_line] 40: ************************************************************************ 765786 [M::ha_hist_line] 41: ****************************************************************************** 827535 [M::ha_hist_line] 42: ************************************************************************************ 890494 [M::ha_hist_line] 43: ***************************************************************************************** 944043 [M::ha_hist_line] 44: ********************************************************************************************* 991836 [M::ha_hist_line] 45: ************************************************************************************************* 1025839 [M::ha_hist_line] 46: *************************************************************************************************** 1048742 [M::ha_hist_line] 47: **************************************************************************************************** 1061516 [M::ha_hist_line] 48: **************************************************************************************************** 1056292 [M::ha_hist_line] 49: ************************************************************************************************** 1036212 [M::ha_hist_line] 50: *********************************************************************************************** 1012698 [M::ha_hist_line] 51: ******************************************************************************************* 970137 [M::ha_hist_line] 52: ************************************************************************************* 905595 [M::ha_hist_line] 53: ******************************************************************************* 839770 [M::ha_hist_line] 54: ************************************************************************ 768707 [M::ha_hist_line] 55: ****************************************************************** 697600 [M::ha_hist_line] 56: ********************************************************** 617135 [M::ha_hist_line] 57: *************************************************** 544752 [M::ha_hist_line] 58: ******************************************** 470427 [M::ha_hist_line] 59: ************************************** 403973 [M::ha_hist_line] 60: ******************************** 344419 [M::ha_hist_line] 61: *************************** 289606 [M::ha_hist_line] 62: *********************** 241088 [M::ha_hist_line] 63: ******************* 200118 [M::ha_hist_line] 64: *************** 163421 [M::ha_hist_line] 65: ************* 133969 [M::ha_hist_line] 66: ********** 106388 [M::ha_hist_line] 67: ******** 85320 [M::ha_hist_line] 68: ****** 68114 [M::ha_hist_line] 69: ***** 55004 [M::ha_hist_line] 70: **** 44422 [M::ha_hist_line] 71: *** 33971 [M::ha_hist_line] 72: *** 27396 [M::ha_hist_line] 73: ** 23463 [M::ha_hist_line] 74: ** 19435 [M::ha_hist_line] 75: ** 16968 [M::ha_hist_line] 76: * 14526 [M::ha_hist_line] 77: * 12884 [M::ha_hist_line] 78: * 11701 [M::ha_hist_line] 79: * 10659 [M::ha_hist_line] 80: * 10251 [M::ha_hist_line] 81: * 9621 [M::ha_hist_line] 82: * 8989 [M::ha_hist_line] 83: * 8549 [M::ha_hist_line] 84: * 8123 [M::ha_hist_line] 85: * 7677 [M::ha_hist_line] 86: * 7812 [M::ha_hist_line] 87: * 7568 [M::ha_hist_line] 88: * 7404 [M::ha_hist_line] 89: * 7565 [M::ha_hist_line] 90: * 7186 [M::ha_hist_line] 91: * 7116 [M::ha_hist_line] 92: * 7026 [M::ha_hist_line] 93: * 7026 [M::ha_hist_line] 94: * 7019 [M::ha_hist_line] 95: * 6803 [M::ha_hist_line] 96: * 6689 [M::ha_hist_line] 97: * 6403 [M::ha_hist_line] 98: * 6308 [M::ha_hist_line] 99: * 6201 [M::ha_hist_line] 100: * 6257 [M::ha_hist_line] 101: * 6056 [M::ha_hist_line] 102: * 5702 [M::ha_hist_line] 103: * 5714 [M::ha_hist_line] 104: * 5514 [M::ha_hist_line] 105: * 5551 [M::ha_hist_line] 106: * 5486 [M::ha_hist_line] rest: **************************** 296075 [M::ha_analyze_count] left: count[23] = 869322 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::9660.77151.26] ==> counted 37722846 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1462314501 minimizers [M::ha_pt_gen::9980.10050.90] ==> indexed 1461886781 positions, counted 37722846 distinct minimizer k-mers

The job is running, so I provide the partial log info until the point I submit the issue.

[chhylp123]

Sorry for the late reply as I was quite busy last month. It should be fine as long as hifiasm could output results. Actually Shane's dataset has similar issue: https://github.com/chhylp123/hifiasm/issues/49#issue-729106823.

[YanCheer]

Sorry for the late reply as I was quite busy last month. It should be fine as long as hifiasm could output results. Actually Shane's dataset has similar issue: #49 (comment).

Thank you for reply~