issues related to the optimization of HiFiasm

[amit4mchiba]

Hi,

Thank you for creating a wonderful tool. I am working on a heterozygous diploid plant genome with size 9.8Gb. Here, I decided to use all HiFi reads, acquired over 25x genome coverage. I used following command for the assembly-

hifiasm -o Nfoetida_hifionly.asm
-k63 -l3 -s 0.5 -t64 -r5 -f38 -D9
--hg-size 9800m --max-kocc 6000
--min-hist-cnt 0 -a6
*.fasta.gz

Here, I had 21 cell worth hifi reads. A typical assembly suggests 20x genome coverage for diploid (10x coverage for HiFi per ploid). As you can see the kmer hist line, the first histogram had follwoing-"[M::ha_ft_gen] peak_hom: 50; peak_het: 10". However, towards the end, this becomes "[M::ha_pt_gen] peak_hom: 30; peak_het: 10". I feel that this is an error as I still feel that the peak_hom should be 50 only. About the peak_hetro, How to judge it in this case?

Do you have any suggestion as what should be done in this case. You help will be highly appreciated. Please find below the HiFiasm run report. [M::ha_analyze_count] lowest: count[5] = 52979246 [M::ha_analyze_count] highest: count[50] = 113129847 [M::ha_hist_line] 2: *************************************************************************************************> 144705980 [M::ha_hist_line] 3: ***************************************************** 59745444 [M::ha_hist_line] 4: ************************************************ 53848050 [M::ha_hist_line] 5: *********************************************** 52979246 [M::ha_hist_line] 6: ************************************************ 53836435 [M::ha_hist_line] 7: ************************************************* 55932739 [M::ha_hist_line] 8: **************************************************** 58463222 [M::ha_hist_line] 9: ***************************************************** 60458588 [M::ha_hist_line] 10: ****************************************************** 60994507 [M::ha_hist_line] 11: ***************************************************** 60288743 [M::ha_hist_line] 12: **************************************************** 58824360 [M::ha_hist_line] 13: ************************************************** 56889595 [M::ha_hist_line] 14: ************************************************* 55319702 [M::ha_hist_line] 15: ************************************************ 53892759 [M::ha_hist_line] 16: *********************************************** 53087948 [M::ha_hist_line] 17: *********************************************** 52823103 [M::ha_hist_line] 18: *********************************************** 52749055 [M::ha_hist_line] 19: *********************************************** 52790018 [M::ha_hist_line] 20: *********************************************** 52677212 [M::ha_hist_line] 21: ********************************************** 52248569 [M::ha_hist_line] 22: ********************************************** 51556652 [M::ha_hist_line] 23: ********************************************* 50483264 [M::ha_hist_line] 24: ******************************************** 49342854 [M::ha_hist_line] 25: ******************************************* 48104623 [M::ha_hist_line] 26: ****************************************** 46998887 [M::ha_hist_line] 27: ***************************************** 45915372 [M::ha_hist_line] 28: **************************************** 45130283 [M::ha_hist_line] 29: **************************************** 44905581 [M::ha_hist_line] 30: **************************************** 45222622 [M::ha_hist_line] 31: ***************************************** 45951849 [M::ha_hist_line] 32: ****************************************** 47332227 [M::ha_hist_line] 33: ******************************************** 49218373 [M::ha_hist_line] 34: ********************************************** 51618941 [M::ha_hist_line] 35: ************************************************ 54594580 [M::ha_hist_line] 36: *************************************************** 58248387 [M::ha_hist_line] 37: ******************************************************* 62392751 [M::ha_hist_line] 38: *********************************************************** 67021804 [M::ha_hist_line] 39: **************************************************************** 71942468 [M::ha_hist_line] 40: ******************************************************************** 77015693 [M::ha_hist_line] 41: ************************************************************************* 82462708 [M::ha_hist_line] 42: ****************************************************************************** 87819183 [M::ha_hist_line] 43: ********************************************************************************** 93174116 [M::ha_hist_line] 44: *************************************************************************************** 98103948 [M::ha_hist_line] 45: ******************************************************************************************* 102555317 [M::ha_hist_line] 46: ********************************************************************************************** 106415207 [M::ha_hist_line] 47: ************************************************************************************************* 109497046 [M::ha_hist_line] 48: *************************************************************************************************** 111643838 [M::ha_hist_line] 49: **************************************************************************************************** 112856623 [M::ha_hist_line] 50: **************************************************************************************************** 113129847 [M::ha_hist_line] 51: *************************************************************************************************** 112541918 [M::ha_hist_line] 52: ************************************************************************************************** 110843390 [M::ha_hist_line] 53: ************************************************************************************************ 108398606 [M::ha_hist_line] 54: ********************************************************************************************* 104835187 [M::ha_hist_line] 55: ***************************************************************************************** 100501981 [M::ha_hist_line] 56: ************************************************************************************ 95550913 [M::ha_hist_line] 57: ******************************************************************************** 90085878 [M::ha_hist_line] 58: ************************************************************************** 83916404 [M::ha_hist_line] 59: ********************************************************************* 77610436 [M::ha_hist_line] 60: *************************************************************** 71050081 [M::ha_hist_line] 61: ********************************************************* 64349068 [M::ha_hist_line] 62: *************************************************** 57685350 [M::ha_hist_line] 63: ********************************************* 51257269 [M::ha_hist_line] 64: **************************************** 45043228 [M::ha_hist_line] 65: *********************************** 39350152 [M::ha_hist_line] 66: ****************************** 33976331 [M::ha_hist_line] 67: ************************** 28983833 [M::ha_hist_line] 68: ********************** 24537664 [M::ha_hist_line] 69: ****************** 20586901 [M::ha_hist_line] 70: *************** 17206696 [M::ha_hist_line] 71: ************* 14265493 [M::ha_hist_line] 72: ********** 11748403 [M::ha_hist_line] 73: ******** 9554514 [M::ha_hist_line] 74: ******* 7766867 [M::ha_hist_line] 75: ****** 6258159 [M::ha_hist_line] 76: ***** 5099343 [M::ha_hist_line] 77: **** 4122194 [M::ha_hist_line] 78: *** 3335758 [M::ha_hist_line] 79: ** 2728826 [M::ha_hist_line] 80: ** 2264879 [M::ha_hist_line] 81: ** 1919829 [M::ha_hist_line] 82: * 1648356 [M::ha_hist_line] 83: * 1448236 [M::ha_hist_line] 84: * 1298447 [M::ha_hist_line] 85: * 1189063 [M::ha_hist_line] 86: * 1099689 [M::ha_hist_line] 87: * 1042383 [M::ha_hist_line] 88: * 990145 [M::ha_hist_line] 89: * 964416 [M::ha_hist_line] 90: * 942051 [M::ha_hist_line] 91: * 934217 [M::ha_hist_line] 92: * 914922 [M::ha_hist_line] 93: * 903429 [M::ha_hist_line] 94: * 892488 [M::ha_hist_line] 95: * 889788 [M::ha_hist_line] 96: * 878726 [M::ha_hist_line] 97: * 871154 [M::ha_hist_line] 98: * 864811 [M::ha_hist_line] 99: * 862608 [M::ha_hist_line] 100: * 856334 [M::ha_hist_line] 101: * 853917 [M::ha_hist_line] 102: * 850322 [M::ha_hist_line] 103: * 830835 [M::ha_hist_line] 104: * 820208 [M::ha_hist_line] 105: * 807020 [M::ha_hist_line] 106: * 792014 [M::ha_hist_line] 107: * 772788 [M::ha_hist_line] 108: * 755796 [M::ha_hist_line] 109: * 736695 [M::ha_hist_line] 110: * 712976 [M::ha_hist_line] 111: * 694973 [M::ha_hist_line] 112: * 678953 [M::ha_hist_line] 113: * 658779 [M::ha_hist_line] 114: * 633979 [M::ha_hist_line] 115: * 612229 [M::ha_hist_line] 116: * 588656 [M::ha_hist_line] rest: ************************ 27677540 [M::ha_analyze_count] left: count[10] = 60994507 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 50; peak_het: 10 [M::ha_ct_shrink::5216.04222.30] ==> counted 3815564 distinct minimizer k-mers [M::ha_ft_gen::5225.428[email protected]] ==> filtered out 3815564 k-mers occurring 450 or more times [M::ha_opt_update_cov] updated max_n_chain to 450 [M::yak_count] collected 1151432308 minimizers [M::yak_count] collected 974719830 minimizers [M::yak_count] collected 220002422 minimizers [M::yak_count] collected 114148561 minimizers [M::yak_count] collected 143372925 minimizers [M::yak_count] collected 120585540 minimizers [M::yak_count] collected 125969842 minimizers [M::yak_count] collected 222364281 minimizers [M::yak_count] collected 207423017 minimizers [M::yak_count] collected 329790720 minimizers [M::yak_count] collected 312530953 minimizers [M::yak_count] collected 261782437 minimizers [M::yak_count] collected 139043690 minimizers [M::yak_count] collected 399099572 minimizers [M::yak_count] collected 739452952 minimizers [M::yak_count] collected 738138968 minimizers [M::yak_count] collected 363634860 minimizers [M::yak_count] collected 420971137 minimizers [M::yak_count] collected 484819274 minimizers [M::yak_count] collected 319643343 minimizers [M::ha_pt_gen::7218.69820.54] ==> counted 631009643 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 2521072 [M::ha_analyze_count] highest: count[49] = 4412660 [M::ha_hist_line] 1: ****************************************************************************************************> 433282802 [M::ha_hist_line] 2: ************************************************************************************************> 9315687 [M::ha_hist_line] 3: ****************************************************************************** 3461774 [M::ha_hist_line] 4: ************************************************************* 2695317 [M::ha_hist_line] 5: ********************************************************* 2529873 [M::ha_hist_line] 6: ********************************************************* 2521072 [M::ha_hist_line] 7: *********************************************************** 2592528 [M::ha_hist_line] 8: ************************************************************* 2681228 [M::ha_hist_line] 9: ************************************************************** 2750511 [M::ha_hist_line] 10: *************************************************************** 2758491 [M::ha_hist_line] 11: ************************************************************** 2715952 [M::ha_hist_line] 12: ************************************************************ 2636097 [M::ha_hist_line] 13: ********************************************************** 2541173 [M::ha_hist_line] 14: ******************************************************** 2462505 [M::ha_hist_line] 15: ****************************************************** 2390888 [M::ha_hist_line] 16: ***************************************************** 2347330 [M::ha_hist_line] 17: ***************************************************** 2323721 [M::ha_hist_line] 18: **************************************************** 2308840 [M::ha_hist_line] 19: **************************************************** 2299513 [M::ha_hist_line] 20: **************************************************** 2283969 [M::ha_hist_line] 21: *************************************************** 2263223 [M::ha_hist_line] 22: ************************************************** 2225563 [M::ha_hist_line] 23: ************************************************* 2176591 [M::ha_hist_line] 24: ************************************************ 2126542 [M::ha_hist_line] 25: *********************************************** 2073304 [M::ha_hist_line] 26: ********************************************** 2026612 [M::ha_hist_line] 27: ********************************************* 1980242 [M::ha_hist_line] 28: ******************************************** 1950327 [M::ha_hist_line] 29: ******************************************** 1940466 [M::ha_hist_line] 30: ******************************************** 1950769 [M::ha_hist_line] 31: ********************************************* 1978526 [M::ha_hist_line] 32: ********************************************** 2032942 [M::ha_hist_line] 33: ************************************************ 2107861 [M::ha_hist_line] 34: ************************************************** 2198118 [M::ha_hist_line] 35: **************************************************** 2314515 [M::ha_hist_line] 36: ******************************************************** 2453151 [M::ha_hist_line] 37: *********************************************************** 2608236 [M::ha_hist_line] 38: *************************************************************** 2781156 [M::ha_hist_line] 39: ******************************************************************* 2966631 [M::ha_hist_line] 40: *********************************************************************** 3153013 [M::ha_hist_line] 41: **************************************************************************** 3359140 [M::ha_hist_line] 42: ********************************************************************************* 3556407 [M::ha_hist_line] 43: ************************************************************************************* 3748478 [M::ha_hist_line] 44: ***************************************************************************************** 3922708 [M::ha_hist_line] 45: ********************************************************************************************* 4081947 [M::ha_hist_line] 46: *********************************************************************************************** 4213257 [M::ha_hist_line] 47: ************************************************************************************************** 4315939 [M::ha_hist_line] 48: *************************************************************************************************** 4379875 [M::ha_hist_line] 49: **************************************************************************************************** 4412660 [M::ha_hist_line] 50: **************************************************************************************************** 4406585 [M::ha_hist_line] 51: *************************************************************************************************** 4364724 [M::ha_hist_line] 52: ************************************************************************************************* 4285931 [M::ha_hist_line] 53: *********************************************************************************************** 4174083 [M::ha_hist_line] 54: ******************************************************************************************* 4021156 [M::ha_hist_line] 55: *************************************************************************************** 3844162 [M::ha_hist_line] 56: *********************************************************************************** 3641963 [M::ha_hist_line] 57: ****************************************************************************** 3421462 [M::ha_hist_line] 58: ************************************************************************ 3177685 [M::ha_hist_line] 59: ****************************************************************** 2929102 [M::ha_hist_line] 60: ************************************************************* 2671279 [M::ha_hist_line] 61: ******************************************************* 2408122 [M::ha_hist_line] 62: ************************************************* 2154707 [M::ha_hist_line] 63: ******************************************* 1907932 [M::ha_hist_line] 64: ************************************** 1673380 [M::ha_hist_line] 65: ********************************* 1457674 [M::ha_hist_line] 66: **************************** 1254713 [M::ha_hist_line] 67: ************************ 1067446 [M::ha_hist_line] 68: ******************** 902557 [M::ha_hist_line] 69: ***************** 757289 [M::ha_hist_line] 70: ************** 631669 [M::ha_hist_line] 71: ************ 525344 [M::ha_hist_line] 72: ********** 433818 [M::ha_hist_line] 73: ******** 353932 [M::ha_hist_line] 74: ******* 288930 [M::ha_hist_line] 75: ***** 234946 [M::ha_hist_line] 76: **** 193807 [M::ha_hist_line] 77: **** 158730 [M::ha_hist_line] 78: *** 130900 [M::ha_hist_line] 79: ** 109751 [M::ha_hist_line] 80: ** 93659 [M::ha_hist_line] 81: ** 81520 [M::ha_hist_line] 82: ** 71214 [M::ha_hist_line] 83: * 64794 [M::ha_hist_line] 84: * 59444 [M::ha_hist_line] 85: * 55626 [M::ha_hist_line] 86: * 52381 [M::ha_hist_line] 87: * 50393 [M::ha_hist_line] 88: * 47850 [M::ha_hist_line] 89: * 47187 [M::ha_hist_line] 90: * 46355 [M::ha_hist_line] 91: * 45808 [M::ha_hist_line] 92: * 45480 [M::ha_hist_line] 93: * 44637 [M::ha_hist_line] 94: * 44137 [M::ha_hist_line] 95: * 44186 [M::ha_hist_line] 96: * 43618 [M::ha_hist_line] 97: * 43242 [M::ha_hist_line] 98: * 42868 [M::ha_hist_line] 99: * 42564 [M::ha_hist_line] 100: * 42446 [M::ha_hist_line] 101: * 41990 [M::ha_hist_line] 102: * 41935 [M::ha_hist_line] 103: * 41205 [M::ha_hist_line] 104: * 40383 [M::ha_hist_line] 105: * 39848 [M::ha_hist_line] 106: * 39289 [M::ha_hist_line] 107: * 38489 [M::ha_hist_line] 108: * 37637 [M::ha_hist_line] 109: * 36805 [M::ha_hist_line] 110: * 36186 [M::ha_hist_line] 111: * 35121 [M::ha_hist_line] 112: * 34443 [M::ha_hist_line] 113: * 33184 [M::ha_hist_line] 114: * 32445 [M::ha_hist_line] 115: * 31538 [M::ha_hist_line] 116: * 30085 [M::ha_hist_line] 117: * 29147 [M::ha_hist_line] 118: * 28402 [M::ha_hist_line] 119: * 27323 [M::ha_hist_line] 120: * 26391 [M::ha_hist_line] 121: * 25372 [M::ha_hist_line] 122: * 24537 [M::ha_hist_line] 123: * 23474 [M::ha_hist_line] 124: * 22599 [M::ha_hist_line] rest: ****************************** 1321157 [M::ha_analyze_count] left: count[10] = 2758491 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 49; peak_het: 10 [M::ha_ct_shrink::7219.60920.54] ==> counted 197726841 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7788926632 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::7917.38922.94] ==> indexed 7355643830 positions, counted 197726841 distinct minimizer k-mers [M::ha_assemble::29700.326[email protected]] ==> corrected reads for round 1 [M::ha_assemble] # bases: 295186006995; # corrected bases: 803886006; # recorrected bases: 546554 [M::ha_assemble] size of buffer: 290.016GB [M::yak_count] collected 7778454260 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::30412.61052.74] ==> counted 418756771 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[3] = 2079646 [M::ha_analyze_count] highest: count[51] = 4318774 [M::ha_hist_line] 1: ************************************************************************************************> 230166213 [M::ha_hist_line] 2: ************************************************************ 2579913 [M::ha_hist_line] 3: ************************************************ 2079646 [M::ha_hist_line] 4: ************************************************** 2168346 [M::ha_hist_line] 5: *************************************************** 2217256 [M::ha_hist_line] 6: ***************************************************** 2298765 [M::ha_hist_line] 7: ******************************************************** 2405786 [M::ha_hist_line] 8: ********************************************************** 2508154 [M::ha_hist_line] 9: ************************************************************ 2600261 [M::ha_hist_line] 10: ************************************************************* 2639418 [M::ha_hist_line] 11: ************************************************************* 2618251 [M::ha_hist_line] 12: *********************************************************** 2563325 [M::ha_hist_line] 13: ********************************************************* 2467718 [M::ha_hist_line] 14: ******************************************************** 2397376 [M::ha_hist_line] 15: ****************************************************** 2328064 [M::ha_hist_line] 16: ***************************************************** 2268343 [M::ha_hist_line] 17: **************************************************** 2248196 [M::ha_hist_line] 18: **************************************************** 2235138 [M::ha_hist_line] 19: **************************************************** 2227026 [M::ha_hist_line] 20: *************************************************** 2221548 [M::ha_hist_line] 21: *************************************************** 2204938 [M::ha_hist_line] 22: *************************************************** 2185738 [M::ha_hist_line] 23: ************************************************** 2146602 [M::ha_hist_line] 24: ************************************************* 2096053 [M::ha_hist_line] 25: *********************************************** 2048799 [M::ha_hist_line] 26: ********************************************** 2004773 [M::ha_hist_line] 27: ********************************************* 1954055 [M::ha_hist_line] 28: ******************************************** 1909036 [M::ha_hist_line] 29: ******************************************** 1883981 [M::ha_hist_line] 30: ******************************************* 1878688 [M::ha_hist_line] 31: ******************************************** 1884381 [M::ha_hist_line] 32: ******************************************** 1913490 [M::ha_hist_line] 33: ********************************************** 1965696 [M::ha_hist_line] 34: *********************************************** 2031399 [M::ha_hist_line] 35: ************************************************* 2113014 [M::ha_hist_line] 36: **************************************************** 2227656 [M::ha_hist_line] 37: ****************************************************** 2351950 [M::ha_hist_line] 38: ********************************************************** 2501911 [M::ha_hist_line] 39: ************************************************************** 2661406 [M::ha_hist_line] 40: ****************************************************************** 2837309 [M::ha_hist_line] 41: ********************************************************************** 3019229 [M::ha_hist_line] 42: ************************************************************************** 3214299 [M::ha_hist_line] 43: ******************************************************************************* 3400312 [M::ha_hist_line] 44: *********************************************************************************** 3588804 [M::ha_hist_line] 45: *************************************************************************************** 3768315 [M::ha_hist_line] 46: ******************************************************************************************* 3934940 [M::ha_hist_line] 47: ********************************************************************************************** 4069359 [M::ha_hist_line] 48: ************************************************************************************************* 4180497 [M::ha_hist_line] 49: *************************************************************************************************** 4263855 [M::ha_hist_line] 50: **************************************************************************************************** 4309686 [M::ha_hist_line] 51: **************************************************************************************************** 4318774 [M::ha_hist_line] 52: **************************************************************************************************** 4300517 [M::ha_hist_line] 53: ************************************************************************************************** 4247066 [M::ha_hist_line] 54: ************************************************************************************************ 4160713 [M::ha_hist_line] 55: ********************************************************************************************* 4029861 [M::ha_hist_line] 56: ****************************************************************************************** 3876315 [M::ha_hist_line] 57: ************************************************************************************** 3699416 [M::ha_hist_line] 58: ********************************************************************************* 3496394 [M::ha_hist_line] 59: **************************************************************************** 3278971 [M::ha_hist_line] 60: ********************************************************************** 3042221 [M::ha_hist_line] 61: ***************************************************************** 2805615 [M::ha_hist_line] 62: *********************************************************** 2544898 [M::ha_hist_line] 63: ***************************************************** 2298717 [M::ha_hist_line] 64: *********************************************** 2050419 [M::ha_hist_line] 65: ****************************************** 1819292 [M::ha_hist_line] 66: ************************************* 1602098 [M::ha_hist_line] 67: ******************************** 1392009 [M::ha_hist_line] 68: **************************** 1196555 [M::ha_hist_line] 69: ************************ 1019855 [M::ha_hist_line] 70: ******************** 860494 [M::ha_hist_line] 71: ***************** 728806 [M::ha_hist_line] 72: ************** 614131 [M::ha_hist_line] 73: ************ 505809 [M::ha_hist_line] 74: ********** 417743 [M::ha_hist_line] 75: ******** 342264 [M::ha_hist_line] 76: ****** 279220 [M::ha_hist_line] 77: ***** 230769 [M::ha_hist_line] 78: **** 189607 [M::ha_hist_line] 79: **** 156515 [M::ha_hist_line] 80: *** 127912 [M::ha_hist_line] 81: ** 107056 [M::ha_hist_line] 82: ** 91416 [M::ha_hist_line] 83: ** 78788 [M::ha_hist_line] 84: ** 70488 [M::ha_hist_line] 85: * 63606 [M::ha_hist_line] 86: * 58585 [M::ha_hist_line] 87: * 54897 [M::ha_hist_line] 88: * 51052 [M::ha_hist_line] 89: * 48499 [M::ha_hist_line] 90: * 47137 [M::ha_hist_line] 91: * 45802 [M::ha_hist_line] 92: * 44538 [M::ha_hist_line] 93: * 44615 [M::ha_hist_line] 94: * 43736 [M::ha_hist_line] 95: * 44001 [M::ha_hist_line] 96: * 43441 [M::ha_hist_line] 97: * 42635 [M::ha_hist_line] 98: * 42546 [M::ha_hist_line] 99: * 41826 [M::ha_hist_line] 100: * 41388 [M::ha_hist_line] 101: * 40993 [M::ha_hist_line] 102: * 41477 [M::ha_hist_line] 103: * 40892 [M::ha_hist_line] 104: * 41043 [M::ha_hist_line] 105: * 40583 [M::ha_hist_line] 106: * 40440 [M::ha_hist_line] 107: * 39874 [M::ha_hist_line] 108: * 38815 [M::ha_hist_line] 109: * 38326 [M::ha_hist_line] 110: * 37023 [M::ha_hist_line] 111: * 36487 [M::ha_hist_line] 112: * 36583 [M::ha_hist_line] 113: * 35010 [M::ha_hist_line] 114: * 34325 [M::ha_hist_line] 115: * 33398 [M::ha_hist_line] 116: * 32903 [M::ha_hist_line] 117: * 31796 [M::ha_hist_line] 118: * 30967 [M::ha_hist_line] 119: * 29404 [M::ha_hist_line] 120: * 29038 [M::ha_hist_line] 121: * 27779 [M::ha_hist_line] 122: * 26522 [M::ha_hist_line] 123: * 25787 [M::ha_hist_line] 124: * 25210 [M::ha_hist_line] 125: * 24696 [M::ha_hist_line] 126: * 23117 [M::ha_hist_line] 127: * 22216 [M::ha_hist_line] rest: ******************************* 1324125 [M::ha_analyze_count] left: count[10] = 2639418 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 30; peak_het: 10 [M::ha_ct_shrink::30413.33852.74] ==> counted 188590558 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7778454260 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::31200.45852.49] ==> indexed 7548288047 positions, counted 188590558 distinct minimizer k-mers [M::ha_assemble::50888.526[email protected]] ==> corrected reads for round 2 [M::ha_assemble] # bases: 295024272112; # corrected bases: 80769951; # recorrected bases: 122854 [M::ha_assemble] size of buffer: 290.964GB [M::yak_count] collected 7776363848 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::51634.32056.65] ==> counted 391698593 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[3] = 1869957 [M::ha_analyze_count] highest: count[51] = 4310303 [M::ha_hist_line] 1: ************************************************************************************************> 203836477 [M::ha_hist_line] 2: ************************************************** 2174225 [M::ha_hist_line] 3: ******************************************* 1869957 [M::ha_hist_line] 4: ************************************************* 2099008 [M::ha_hist_line] 5: *************************************************** 2178868 [M::ha_hist_line] 6: ***************************************************** 2277572 [M::ha_hist_line] 7: ******************************************************* 2388427 [M::ha_hist_line] 8: ********************************************************** 2493399 [M::ha_hist_line] 9: ************************************************************ 2586973 [M::ha_hist_line] 10: ************************************************************* 2628249 [M::ha_hist_line] 11: ************************************************************* 2609165 [M::ha_hist_line] 12: *********************************************************** 2555289 [M::ha_hist_line] 13: ********************************************************* 2462221 [M::ha_hist_line] 14: ******************************************************* 2389665 [M::ha_hist_line] 15: ****************************************************** 2321242 [M::ha_hist_line] 16: **************************************************** 2261956 [M::ha_hist_line] 17: **************************************************** 2241299 [M::ha_hist_line] 18: **************************************************** 2228433 [M::ha_hist_line] 19: **************************************************** 2221851 [M::ha_hist_line] 20: *************************************************** 2213725 [M::ha_hist_line] 21: *************************************************** 2199390 [M::ha_hist_line] 22: *************************************************** 2181002 [M::ha_hist_line] 23: ************************************************** 2140688 [M::ha_hist_line] 24: ************************************************* 2090849 [M::ha_hist_line] 25: *********************************************** 2041099 [M::ha_hist_line] 26: ********************************************** 2002405 [M::ha_hist_line] 27: ********************************************* 1946740 [M::ha_hist_line] 28: ******************************************** 1900820 [M::ha_hist_line] 29: ******************************************* 1873867 [M::ha_hist_line] 30: ******************************************* 1868806 [M::ha_hist_line] 31: ******************************************* 1870414 [M::ha_hist_line] 32: ******************************************** 1897586 [M::ha_hist_line] 33: ********************************************* 1946652 [M::ha_hist_line] 34: *********************************************** 2009808 [M::ha_hist_line] 35: ************************************************ 2089589 [M::ha_hist_line] 36: *************************************************** 2199321 [M::ha_hist_line] 37: ****************************************************** 2321957 [M::ha_hist_line] 38: ********************************************************* 2466584 [M::ha_hist_line] 39: ************************************************************* 2627024 [M::ha_hist_line] 40: ***************************************************************** 2796199 [M::ha_hist_line] 41: ********************************************************************* 2980155 [M::ha_hist_line] 42: ************************************************************************** 3169418 [M::ha_hist_line] 43: ****************************************************************************** 3359234 [M::ha_hist_line] 44: ********************************************************************************** 3550425 [M::ha_hist_line] 45: *************************************************************************************** 3729374 [M::ha_hist_line] 46: ****************************************************************************************** 3898830 [M::ha_hist_line] 47: ********************************************************************************************** 4040602 [M::ha_hist_line] 48: ************************************************************************************************ 4152670 [M::ha_hist_line] 49: ************************************************************************************************** 4244176 [M::ha_hist_line] 50: **************************************************************************************************** 4299235 [M::ha_hist_line] 51: **************************************************************************************************** 4310303 [M::ha_hist_line] 52: **************************************************************************************************** 4299310 [M::ha_hist_line] 53: *************************************************************************************************** 4254703 [M::ha_hist_line] 54: ************************************************************************************************* 4172504 [M::ha_hist_line] 55: ********************************************************************************************** 4047116 [M::ha_hist_line] 56: ******************************************************************************************* 3907095 [M::ha_hist_line] 57: *************************************************************************************** 3732028 [M::ha_hist_line] 58: ********************************************************************************** 3530571 [M::ha_hist_line] 59: ***************************************************************************** 3317906 [M::ha_hist_line] 60: ************************************************************************ 3085803 [M::ha_hist_line] 61: ****************************************************************** 2854381 [M::ha_hist_line] 62: ************************************************************ 2588186 [M::ha_hist_line] 63: ****************************************************** 2348830 [M::ha_hist_line] 64: ************************************************* 2096858 [M::ha_hist_line] 65: ******************************************* 1864744 [M::ha_hist_line] 66: ************************************** 1642189 [M::ha_hist_line] 67: ********************************* 1433307 [M::ha_hist_line] 68: ***************************** 1233011 [M::ha_hist_line] 69: ************************ 1054414 [M::ha_hist_line] 70: ********************* 891435 [M::ha_hist_line] 71: ****************** 755720 [M::ha_hist_line] 72: *************** 637524 [M::ha_hist_line] 73: ************ 526912 [M::ha_hist_line] 74: ********** 435094 [M::ha_hist_line] 75: ******** 357059 [M::ha_hist_line] 76: ******* 292008 [M::ha_hist_line] 77: ****** 239742 [M::ha_hist_line] 78: ***** 197600 [M::ha_hist_line] 79: **** 163090 [M::ha_hist_line] 80: *** 133910 [M::ha_hist_line] 81: *** 111040 [M::ha_hist_line] 82: ** 94150 [M::ha_hist_line] 83: ** 81050 [M::ha_hist_line] 84: ** 72289 [M::ha_hist_line] 85: ** 65172 [M::ha_hist_line] 86: * 59121 [M::ha_hist_line] 87: * 55220 [M::ha_hist_line] 88: * 51517 [M::ha_hist_line] 89: * 48983 [M::ha_hist_line] 90: * 47479 [M::ha_hist_line] 91: * 45930 [M::ha_hist_line] 92: * 44482 [M::ha_hist_line] 93: * 44580 [M::ha_hist_line] 94: * 43632 [M::ha_hist_line] 95: * 44076 [M::ha_hist_line] 96: * 43100 [M::ha_hist_line] 97: * 42473 [M::ha_hist_line] 98: * 42729 [M::ha_hist_line] 99: * 42046 [M::ha_hist_line] 100: * 41598 [M::ha_hist_line] 101: * 41013 [M::ha_hist_line] 102: * 41261 [M::ha_hist_line] 103: * 40884 [M::ha_hist_line] 104: * 40811 [M::ha_hist_line] 105: * 40657 [M::ha_hist_line] 106: * 40508 [M::ha_hist_line] 107: * 40166 [M::ha_hist_line] 108: * 38860 [M::ha_hist_line] 109: * 38312 [M::ha_hist_line] 110: * 37444 [M::ha_hist_line] 111: * 36800 [M::ha_hist_line] 112: * 36316 [M::ha_hist_line] 113: * 35249 [M::ha_hist_line] 114: * 34669 [M::ha_hist_line] 115: * 33536 [M::ha_hist_line] 116: * 32965 [M::ha_hist_line] 117: * 31888 [M::ha_hist_line] 118: * 31634 [M::ha_hist_line] 119: * 29776 [M::ha_hist_line] 120: * 29276 [M::ha_hist_line] 121: * 27741 [M::ha_hist_line] 122: * 27288 [M::ha_hist_line] 123: * 25859 [M::ha_hist_line] 124: * 25610 [M::ha_hist_line] 125: * 24899 [M::ha_hist_line] 126: * 23740 [M::ha_hist_line] 127: * 22283 [M::ha_hist_line] 128: * 21710 [M::ha_hist_line] rest: ****************************** 1310498 [M::ha_analyze_count] left: count[10] = 2628249 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 30; peak_het: 10 [M::ha_ct_shrink::51634.78956.65] ==> counted 187862116 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7776363848 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::52426.36156.43] ==> indexed 7572527371 positions, counted 187862116 distinct minimizer k-mers [M::ha_assemble::71331.543[email protected]] ==> corrected reads for round 3 [M::ha_assemble] # bases: 295008893499; # corrected bases: 8355462; # recorrected bases: 130435 [M::ha_assemble] size of buffer: 290.827GB [M::yak_count] collected 7775570958 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::72012.75058.28] ==> counted 388934680 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[3] = 1801303 [M::ha_analyze_count] highest: count[51] = 4310869 [M::ha_hist_line] 1: ************************************************************************************************> 201288609 [M::ha_hist_line] 2: ************************************************ 2079494 [M::ha_hist_line] 3: ****************************************** 1801303 [M::ha_hist_line] 4: ************************************************ 2082781 [M::ha_hist_line] 5: ************************************************** 2168320 [M::ha_hist_line] 6: ***************************************************** 2270773 [M::ha_hist_line] 7: ******************************************************* 2383254 [M::ha_hist_line] 8: ********************************************************** 2488389 [M::ha_hist_line] 9: ************************************************************ 2583334 [M::ha_hist_line] 10: ************************************************************* 2626196 [M::ha_hist_line] 11: ************************************************************ 2606338 [M::ha_hist_line] 12: *********************************************************** 2553238 [M::ha_hist_line] 13: ********************************************************* 2460669 [M::ha_hist_line] 14: ******************************************************* 2387838 [M::ha_hist_line] 15: ****************************************************** 2319492 [M::ha_hist_line] 16: **************************************************** 2260354 [M::ha_hist_line] 17: **************************************************** 2239367 [M::ha_hist_line] 18: **************************************************** 2227267 [M::ha_hist_line] 19: **************************************************** 2220250 [M::ha_hist_line] 20: *************************************************** 2213170 [M::ha_hist_line] 21: *************************************************** 2198494 [M::ha_hist_line] 22: *************************************************** 2180111 [M::ha_hist_line] 23: ************************************************** 2139196 [M::ha_hist_line] 24: ************************************************ 2089146 [M::ha_hist_line] 25: *********************************************** 2040247 [M::ha_hist_line] 26: ********************************************** 2001583 [M::ha_hist_line] 27: ********************************************* 1946102 [M::ha_hist_line] 28: ******************************************** 1899834 [M::ha_hist_line] 29: ******************************************* 1873184 [M::ha_hist_line] 30: ******************************************* 1867295 [M::ha_hist_line] 31: ******************************************* 1868424 [M::ha_hist_line] 32: ******************************************** 1896654 [M::ha_hist_line] 33: ********************************************* 1944180 [M::ha_hist_line] 34: *********************************************** 2008261 [M::ha_hist_line] 35: ************************************************ 2087274 [M::ha_hist_line] 36: *************************************************** 2196479 [M::ha_hist_line] 37: ****************************************************** 2319269 [M::ha_hist_line] 38: ********************************************************* 2463674 [M::ha_hist_line] 39: ************************************************************* 2624227 [M::ha_hist_line] 40: ***************************************************************** 2791677 [M::ha_hist_line] 41: ********************************************************************* 2977072 [M::ha_hist_line] 42: ************************************************************************* 3166686 [M::ha_hist_line] 43: ****************************************************************************** 3356089 [M::ha_hist_line] 44: ********************************************************************************** 3546845 [M::ha_hist_line] 45: ************************************************************************************** 3725641 [M::ha_hist_line] 46: ****************************************************************************************** 3895591 [M::ha_hist_line] 47: ********************************************************************************************** 4039031 [M::ha_hist_line] 48: ************************************************************************************************ 4151421 [M::ha_hist_line] 49: ************************************************************************************************** 4241681 [M::ha_hist_line] 50: **************************************************************************************************** 4298239 [M::ha_hist_line] 51: **************************************************************************************************** 4310869 [M::ha_hist_line] 52: **************************************************************************************************** 4298356 [M::ha_hist_line] 53: *************************************************************************************************** 4255131 [M::ha_hist_line] 54: ************************************************************************************************* 4174557 [M::ha_hist_line] 55: ********************************************************************************************** 4049436 [M::ha_hist_line] 56: ******************************************************************************************* 3909836 [M::ha_hist_line] 57: *************************************************************************************** 3734395 [M::ha_hist_line] 58: ********************************************************************************** 3535359 [M::ha_hist_line] 59: ***************************************************************************** 3321440 [M::ha_hist_line] 60: ************************************************************************ 3089000 [M::ha_hist_line] 61: ****************************************************************** 2859447 [M::ha_hist_line] 62: ************************************************************ 2592683 [M::ha_hist_line] 63: ******************************************************* 2353182 [M::ha_hist_line] 64: ************************************************* 2101998 [M::ha_hist_line] 65: ******************************************* 1868269 [M::ha_hist_line] 66: ************************************** 1644895 [M::ha_hist_line] 67: ********************************* 1437223 [M::ha_hist_line] 68: ***************************** 1236493 [M::ha_hist_line] 69: ************************* 1057824 [M::ha_hist_line] 70: ********************* 893738 [M::ha_hist_line] 71: ****************** 757995 [M::ha_hist_line] 72: *************** 639829 [M::ha_hist_line] 73: ************ 528871 [M::ha_hist_line] 74: ********** 436553 [M::ha_hist_line] 75: ******** 358201 [M::ha_hist_line] 76: ******* 293260 [M::ha_hist_line] 77: ****** 240828 [M::ha_hist_line] 78: ***** 198353 [M::ha_hist_line] 79: **** 163580 [M::ha_hist_line] 80: *** 134491 [M::ha_hist_line] 81: *** 111452 [M::ha_hist_line] 82: ** 94543 [M::ha_hist_line] 83: ** 81265 [M::ha_hist_line] 84: ** 72347 [M::ha_hist_line] 85: ** 65124 [M::ha_hist_line] 86: * 59394 [M::ha_hist_line] 87: * 55099 [M::ha_hist_line] 88: * 51474 [M::ha_hist_line] 89: * 49060 [M::ha_hist_line] 90: * 47347 [M::ha_hist_line] 91: * 45954 [M::ha_hist_line] 92: * 44651 [M::ha_hist_line] 93: * 44519 [M::ha_hist_line] 94: * 43745 [M::ha_hist_line] 95: * 43932 [M::ha_hist_line] 96: * 43065 [M::ha_hist_line] 97: * 42353 [M::ha_hist_line] 98: * 42746 [M::ha_hist_line] 99: * 41906 [M::ha_hist_line] 100: * 41685 [M::ha_hist_line] 101: * 40798 [M::ha_hist_line] 102: * 41412 [M::ha_hist_line] 103: * 40859 [M::ha_hist_line] 104: * 40735 [M::ha_hist_line] 105: * 40744 [M::ha_hist_line] 106: * 40377 [M::ha_hist_line] 107: * 40241 [M::ha_hist_line] 108: * 38795 [M::ha_hist_line] 109: * 38529 [M::ha_hist_line] 110: * 37365 [M::ha_hist_line] 111: * 36777 [M::ha_hist_line] 112: * 36403 [M::ha_hist_line] 113: * 35093 [M::ha_hist_line] 114: * 34831 [M::ha_hist_line] 115: * 33775 [M::ha_hist_line] 116: * 33036 [M::ha_hist_line] 117: * 31771 [M::ha_hist_line] 118: * 31597 [M::ha_hist_line] 119: * 29983 [M::ha_hist_line] 120: * 29297 [M::ha_hist_line] 121: * 27861 [M::ha_hist_line] 122: * 27035 [M::ha_hist_line] 123: * 25945 [M::ha_hist_line] 124: * 25530 [M::ha_hist_line] 125: * 24977 [M::ha_hist_line] 126: * 23666 [M::ha_hist_line] 127: * 22260 [M::ha_hist_line] 128: * 21654 [M::ha_hist_line] rest: ****************************** 1311538 [M::ha_analyze_count] left: count[10] = 2626196 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 30; peak_het: 10 [M::ha_ct_shrink::72013.22658.28] ==> counted 187646071 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7775570958 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::72745.14358.15] ==> indexed 7574282349 positions, counted 187646071 distinct minimizer k-mers [M::ha_assemble::92493.121[email protected]] ==> corrected reads for round 4 [M::ha_assemble] # bases: 295007587848; # corrected bases: 2049217; # recorrected bases: 75177 [M::ha_assemble] size of buffer: 291.367GB [M::yak_count] collected 7775197348 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::93174.96459.26] ==> counted 388295018 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[3] = 1773705 [M::ha_analyze_count] highest: count[51] = 4310899 [M::ha_hist_line] 1: ************************************************************************************************> 200752511 [M::ha_hist_line] 2: *********************************************** 2033142 [M::ha_hist_line] 3: ***************************************** 1773705 [M::ha_hist_line] 4: ************************************************ 2074863 [M::ha_hist_line] 5: ************************************************** 2162454 [M::ha_hist_line] 6: ***************************************************** 2267415 [M::ha_hist_line] 7: ******************************************************* 2380829 [M::ha_hist_line] 8: ********************************************************** 2486798 [M::ha_hist_line] 9: ************************************************************ 2581522 [M::ha_hist_line] 10: ************************************************************* 2624556 [M::ha_hist_line] 11: ************************************************************ 2605296 [M::ha_hist_line] 12: *********************************************************** 2552188 [M::ha_hist_line] 13: ********************************************************* 2459929 [M::ha_hist_line] 14: ******************************************************* 2386678 [M::ha_hist_line] 15: ****************************************************** 2318769 [M::ha_hist_line] 16: **************************************************** 2259523 [M::ha_hist_line] 17: **************************************************** 2238862 [M::ha_hist_line] 18: **************************************************** 2226825 [M::ha_hist_line] 19: *************************************************** 2219630 [M::ha_hist_line] 20: *************************************************** 2212836 [M::ha_hist_line] 21: *************************************************** 2197901 [M::ha_hist_line] 22: *************************************************** 2179438 [M::ha_hist_line] 23: ************************************************** 2139088 [M::ha_hist_line] 24: ************************************************ 2088726 [M::ha_hist_line] 25: *********************************************** 2039853 [M::ha_hist_line] 26: ********************************************** 2001408 [M::ha_hist_line] 27: ********************************************* 1945921 [M::ha_hist_line] 28: ******************************************** 1899720 [M::ha_hist_line] 29: ******************************************* 1872724 [M::ha_hist_line] 30: ******************************************* 1867277 [M::ha_hist_line] 31: ******************************************* 1868328 [M::ha_hist_line] 32: ******************************************** 1896400 [M::ha_hist_line] 33: ********************************************* 1943961 [M::ha_hist_line] 34: *********************************************** 2007736 [M::ha_hist_line] 35: ************************************************ 2086261 [M::ha_hist_line] 36: *************************************************** 2195873 [M::ha_hist_line] 37: ****************************************************** 2319057 [M::ha_hist_line] 38: ********************************************************* 2463419 [M::ha_hist_line] 39: ************************************************************* 2623528 [M::ha_hist_line] 40: ***************************************************************** 2791250 [M::ha_hist_line] 41: ********************************************************************* 2976135 [M::ha_hist_line] 42: ************************************************************************* 3165703 [M::ha_hist_line] 43: ****************************************************************************** 3355461 [M::ha_hist_line] 44: ********************************************************************************** 3546604 [M::ha_hist_line] 45: ************************************************************************************** 3724739 [M::ha_hist_line] 46: ****************************************************************************************** 3895511 [M::ha_hist_line] 47: ********************************************************************************************** 4038334 [M::ha_hist_line] 48: ************************************************************************************************ 4150890 [M::ha_hist_line] 49: ************************************************************************************************** 4241812 [M::ha_hist_line] 50: **************************************************************************************************** 4297733 [M::ha_hist_line] 51: **************************************************************************************************** 4310899 [M::ha_hist_line] 52: **************************************************************************************************** 4298566 [M::ha_hist_line] 53: *************************************************************************************************** 4254953 [M::ha_hist_line] 54: ************************************************************************************************* 4174939 [M::ha_hist_line] 55: ********************************************************************************************** 4049868 [M::ha_hist_line] 56: ******************************************************************************************* 3910496 [M::ha_hist_line] 57: *************************************************************************************** 3734471 [M::ha_hist_line] 58: ********************************************************************************** 3535821 [M::ha_hist_line] 59: ***************************************************************************** 3322316 [M::ha_hist_line] 60: ************************************************************************ 3090074 [M::ha_hist_line] 61: ****************************************************************** 2860263 [M::ha_hist_line] 62: ************************************************************ 2593601 [M::ha_hist_line] 63: ******************************************************* 2354208 [M::ha_hist_line] 64: ************************************************* 2102808 [M::ha_hist_line] 65: ******************************************* 1869130 [M::ha_hist_line] 66: ************************************** 1645627 [M::ha_hist_line] 67: ********************************* 1438504 [M::ha_hist_line] 68: ***************************** 1237010 [M::ha_hist_line] 69: ************************* 1058343 [M::ha_hist_line] 70: ********************* 894372 [M::ha_hist_line] 71: ****************** 758542 [M::ha_hist_line] 72: *************** 640079 [M::ha_hist_line] 73: ************ 529317 [M::ha_hist_line] 74: ********** 436879 [M::ha_hist_line] 75: ******** 358315 [M::ha_hist_line] 76: ******* 293473 [M::ha_hist_line] 77: ****** 240938 [M::ha_hist_line] 78: ***** 198536 [M::ha_hist_line] 79: **** 163976 [M::ha_hist_line] 80: *** 134231 [M::ha_hist_line] 81: *** 111736 [M::ha_hist_line] 82: ** 94560 [M::ha_hist_line] 83: ** 81166 [M::ha_hist_line] 84: ** 72356 [M::ha_hist_line] 85: ** 65190 [M::ha_hist_line] 86: * 59320 [M::ha_hist_line] 87: * 55199 [M::ha_hist_line] 88: * 51507 [M::ha_hist_line] 89: * 49078 [M::ha_hist_line] 90: * 47376 [M::ha_hist_line] 91: * 46009 [M::ha_hist_line] 92: * 44565 [M::ha_hist_line] 93: * 44535 [M::ha_hist_line] 94: * 43656 [M::ha_hist_line] 95: * 44008 [M::ha_hist_line] 96: * 43091 [M::ha_hist_line] 97: * 42304 [M::ha_hist_line] 98: * 42780 [M::ha_hist_line] 99: * 42081 [M::ha_hist_line] 100: * 41588 [M::ha_hist_line] 101: * 40987 [M::ha_hist_line] 102: * 41321 [M::ha_hist_line] 103: * 40953 [M::ha_hist_line] 104: * 40679 [M::ha_hist_line] 105: * 40684 [M::ha_hist_line] 106: * 40353 [M::ha_hist_line] 107: * 40354 [M::ha_hist_line] 108: * 38840 [M::ha_hist_line] 109: * 38417 [M::ha_hist_line] 110: * 37326 [M::ha_hist_line] 111: * 36993 [M::ha_hist_line] 112: * 36261 [M::ha_hist_line] 113: * 35133 [M::ha_hist_line] 114: * 34793 [M::ha_hist_line] 115: * 33710 [M::ha_hist_line] 116: * 32935 [M::ha_hist_line] 117: * 31795 [M::ha_hist_line] 118: * 31709 [M::ha_hist_line] 119: * 29854 [M::ha_hist_line] 120: * 29310 [M::ha_hist_line] 121: * 27848 [M::ha_hist_line] 122: * 27196 [M::ha_hist_line] 123: * 25977 [M::ha_hist_line] 124: * 25598 [M::ha_hist_line] 125: * 24850 [M::ha_hist_line] 126: * 23764 [M::ha_hist_line] 127: * 22337 [M::ha_hist_line] 128: * 21664 [M::ha_hist_line] rest: ****************************** 1311595 [M::ha_analyze_count] left: count[10] = 2624556 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 30; peak_het: 10 [M::ha_ct_shrink::93175.46859.26] ==> counted 187542507 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7775197348 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::93873.05559.16] ==> indexed 7574444837 positions, counted 187542507 distinct minimizer k-mers [M::ha_assemble::113625.444[email protected]] ==> corrected reads for round 5 [M::ha_assemble] # bases: 295007263243; # corrected bases: 814853; # recorrected bases: 54019 [M::ha_assemble] size of buffer: 290.433GB [M::yak_count] collected 7774960431 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::114311.00559.89] ==> counted 388041269 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[3] = 1760580 [M::ha_analyze_count] highest: count[51] = 4310595 [M::ha_hist_line] 1: *************************************************************************************************> 200553753 [M::ha_hist_line] 2: *********************************************** 2008261 [M::ha_hist_line] 3: ***************************************** 1760580 [M::ha_hist_line] 4: ************************************************ 2070382 [M::ha_hist_line] 5: ************************************************** 2159021 [M::ha_hist_line] 6: ***************************************************** 2265265 [M::ha_hist_line] 7: ******************************************************* 2379746 [M::ha_hist_line] 8: ********************************************************** 2485753 [M::ha_hist_line] 9: ************************************************************ 2580472 [M::ha_hist_line] 10: ************************************************************* 2623607 [M::ha_hist_line] 11: ************************************************************ 2604845 [M::ha_hist_line] 12: *********************************************************** 2551926 [M::ha_hist_line] 13: ********************************************************* 2459231 [M::ha_hist_line] 14: ******************************************************* 2386418 [M::ha_hist_line] 15: ****************************************************** 2318481 [M::ha_hist_line] 16: **************************************************** 2259044 [M::ha_hist_line] 17: **************************************************** 2238546 [M::ha_hist_line] 18: **************************************************** 2226628 [M::ha_hist_line] 19: *************************************************** 2219362 [M::ha_hist_line] 20: *************************************************** 2212538 [M::ha_hist_line] 21: *************************************************** 2197496 [M::ha_hist_line] 22: *************************************************** 2179514 [M::ha_hist_line] 23: ************************************************** 2139028 [M::ha_hist_line] 24: ************************************************ 2088638 [M::ha_hist_line] 25: *********************************************** 2039641 [M::ha_hist_line] 26: ********************************************** 2001279 [M::ha_hist_line] 27: ********************************************* 1945824 [M::ha_hist_line] 28: ******************************************** 1899388 [M::ha_hist_line] 29: ******************************************* 1872616 [M::ha_hist_line] 30: ******************************************* 1867025 [M::ha_hist_line] 31: ******************************************* 1868413 [M::ha_hist_line] 32: ******************************************** 1896211 [M::ha_hist_line] 33: ********************************************* 1943718 [M::ha_hist_line] 34: *********************************************** 2007734 [M::ha_hist_line] 35: ************************************************ 2086168 [M::ha_hist_line] 36: *************************************************** 2195629 [M::ha_hist_line] 37: ****************************************************** 2318827 [M::ha_hist_line] 38: ********************************************************* 2463349 [M::ha_hist_line] 39: ************************************************************* 2623353 [M::ha_hist_line] 40: ***************************************************************** 2791292 [M::ha_hist_line] 41: ********************************************************************* 2975795 [M::ha_hist_line] 42: ************************************************************************* 3165469 [M::ha_hist_line] 43: ****************************************************************************** 3355496 [M::ha_hist_line] 44: ********************************************************************************** 3546446 [M::ha_hist_line] 45: ************************************************************************************** 3724393 [M::ha_hist_line] 46: ****************************************************************************************** 3894946 [M::ha_hist_line] 47: ********************************************************************************************** 4038427 [M::ha_hist_line] 48: ************************************************************************************************ 4151022 [M::ha_hist_line] 49: ************************************************************************************************** 4242036 [M::ha_hist_line] 50: **************************************************************************************************** 4297999 [M::ha_hist_line] 51: **************************************************************************************************** 4310595 [M::ha_hist_line] 52: **************************************************************************************************** 4298218 [M::ha_hist_line] 53: *************************************************************************************************** 4254977 [M::ha_hist_line] 54: ************************************************************************************************* 4175316 [M::ha_hist_line] 55: ********************************************************************************************** 4050121 [M::ha_hist_line] 56: ******************************************************************************************* 3910440 [M::ha_hist_line] 57: *************************************************************************************** 3734573 [M::ha_hist_line] 58: ********************************************************************************** 3536070 [M::ha_hist_line] 59: ***************************************************************************** 3322595 [M::ha_hist_line] 60: ************************************************************************ 3090337 [M::ha_hist_line] 61: ****************************************************************** 2860624 [M::ha_hist_line] 62: ************************************************************ 2593930 [M::ha_hist_line] 63: ******************************************************* 2354388 [M::ha_hist_line] 64: ************************************************* 2103089 [M::ha_hist_line] 65: ******************************************* 1869397 [M::ha_hist_line] 66: ************************************** 1645933 [M::ha_hist_line] 67: ********************************* 1438782 [M::ha_hist_line] 68: ***************************** 1237250 [M::ha_hist_line] 69: ************************* 1058606 [M::ha_hist_line] 70: ********************* 894409 [M::ha_hist_line] 71: ****************** 758540 [M::ha_hist_line] 72: *************** 640181 [M::ha_hist_line] 73: ************ 529608 [M::ha_hist_line] 74: ********** 437016 [M::ha_hist_line] 75: ******** 358324 [M::ha_hist_line] 76: ******* 293498 [M::ha_hist_line] 77: ****** 241049 [M::ha_hist_line] 78: ***** 198571 [M::ha_hist_line] 79: **** 164080 [M::ha_hist_line] 80: *** 134234 [M::ha_hist_line] 81: *** 111715 [M::ha_hist_line] 82: ** 94580 [M::ha_hist_line] 83: ** 81225 [M::ha_hist_line] 84: ** 72352 [M::ha_hist_line] 85: ** 65161 [M::ha_hist_line] 86: * 59366 [M::ha_hist_line] 87: * 55177 [M::ha_hist_line] 88: * 51549 [M::ha_hist_line] 89: * 49109 [M::ha_hist_line] 90: * 47344 [M::ha_hist_line] 91: * 46002 [M::ha_hist_line] 92: * 44567 [M::ha_hist_line] 93: * 44575 [M::ha_hist_line] 94: * 43639 [M::ha_hist_line] 95: * 44006 [M::ha_hist_line] 96: * 43106 [M::ha_hist_line] 97: * 42288 [M::ha_hist_line] 98: * 42775 [M::ha_hist_line] 99: * 42077 [M::ha_hist_line] 100: * 41603 [M::ha_hist_line] 101: * 40952 [M::ha_hist_line] 102: * 41329 [M::ha_hist_line] 103: * 40920 [M::ha_hist_line] 104: * 40699 [M::ha_hist_line] 105: * 40704 [M::ha_hist_line] 106: * 40354 [M::ha_hist_line] 107: * 40363 [M::ha_hist_line] 108: * 38786 [M::ha_hist_line] 109: * 38420 [M::ha_hist_line] 110: * 37355 [M::ha_hist_line] 111: * 37026 [M::ha_hist_line] 112: * 36254 [M::ha_hist_line] 113: * 35125 [M::ha_hist_line] 114: * 34784 [M::ha_hist_line] 115: * 33728 [M::ha_hist_line] 116: * 32932 [M::ha_hist_line] 117: * 31815 [M::ha_hist_line] 118: * 31723 [M::ha_hist_line] 119: * 29797 [M::ha_hist_line] 120: * 29310 [M::ha_hist_line] 121: * 27855 [M::ha_hist_line] 122: * 27197 [M::ha_hist_line] 123: * 25985 [M::ha_hist_line] 124: * 25616 [M::ha_hist_line] 125: * 24809 [M::ha_hist_line] 126: * 23745 [M::ha_hist_line] 127: * 22382 [M::ha_hist_line] 128: * 21633 [M::ha_hist_line] rest: ****************************** 1311673 [M::ha_analyze_count] left: count[10] = 2623607 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 30; peak_het: 10 [M::ha_ct_shrink::114311.49759.89] ==> counted 187487516 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7774960431 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::115085.35059.78] ==> indexed 7574406678 positions, counted 187487516 distinct minimizer k-mers [M::ha_assemble::123332.430[email protected]] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 595131794 [M::ha_print_ovlp_stat] # strong overlaps: 524566409 [M::ha_print_ovlp_stat] # weak overlaps: 70565385 [M::ha_print_ovlp_stat] # exact overlaps: 562634832 [M::ha_print_ovlp_stat] # inexact overlaps: 32496962 [M::ha_print_ovlp_stat] # overlaps without large indels: 593278516 [M::ha_print_ovlp_stat] # reverse overlaps: 836899307 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: 29 [M::purge_dups] purge duplication coverage threshold: 37 Writing raw unitig GFA to disk... Writing processed unitig GFA to disk... [M::purge_dups] homozygous read coverage threshold: 29 [M::purge_dups] purge duplication coverage threshold: 37 [M::mc_solve_core::13.765] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [24, infinity] Writing Amit_genome__hifionly.asm.bp.p_ctg.gfa to disk... [M::adjust_utg_by_trio] primary contig coverage range: [24, infinity] Writing Amit_genome__hifionly.asm.bp.hap1.p_ctg.gfa to disk... [M::adjust_utg_by_trio] primary contig coverage range: [24, infinity] Writing Amit_genome__hifionly.asm.bp.hap2.p_ctg.gfa to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.16.1-r375 [M::main] CMD: hifiasm -o Amit_genome__hifionly.asm -k63 -l3 -s 0.5 -t64 -r5 -f38 -D9 --hg-size 9800m --max-kocc 6000 --min-hist-cnt 0 -a6 m64106_220108_230543.hifi_reads.fasta.gz m64106_220117_195515.hifi_reads.fasta.gz m64124_201021_154155.ccs.fasta.gz m64124_201130_095036.ccs.fasta.gz m64124_201201_160550.ccs.fasta.gz m64124_201202_223424.ccs.fasta.gz m64124_201204_050257.ccs.fasta.gz m64124_210402_112945.ccs.fasta.gz m64124_210403_174444.ccs.fasta.gz m64124_210405_001231.ccs.fasta.gz m64216e_210210_192044.hifi_reads.fasta.gz m64216e_210216_084230.hifi_reads.fasta.gz m64216e_210217_145040.hifi_reads.fasta.gz m64216e_210218_211150.hifi_reads.fasta.gz m64216e_210331_161541.hifi_reads.fasta.gz Maybe_Testing_check_Kyoto_line_m64124_210513_162944.ccs.fasta.gz Amit_genome__Cell1.fasta.gz Amit_genome__Cell2.fasta.gz Amit_genome__Cell3.fasta.gz Amit_genome__Cell4.fasta.gz [M::main] Real time: 127670.774 sec; CPU: 7413000.571 sec; Peak RSS: 870.691 GB

[lh3]

m64124_201130_095036.ccs.fasta.gz m64124_201201_160550.ccs.fasta.gz

Are these HiFi reads or just CCS reads? HiFi reads are high-quality CCS reads.

Maybe_Testing_check_Kyoto_line_m64124_210513_162944.ccs.fasta.gz Amit_genome__Cell1.fasta.gz

Are these sequenced from exactly the same sample? Why do your files have a variety of file names? Please make sure you use HiFi reads for the same diploid sample. It will be hard for hifiasm to get a good assembly with your current data where you see a high fraction of recurrent sequencing errors and a huge number of singleton k-mers even in the last round of error correction – ordinary HiFi data don't look like this.

[amit4mchiba]

Thank you so much for such a quick reply.

Actually I got HiFi sequencing for same sample but through different providers and at different time points. And the reads that they gave me were named as ccs or hifi. So, you think that it could be that the ccs and hifi are different kind of reads and hence this histogram? I guess the method used for the conversion of subreads to hifi needs to be the same, and therefore, this could be the cause if this funny looking kmer plot, isn't it? I will re-run the hifi reads conversion and again run hifiasm. Will get back to you with new run results. Thanks again.

[chhylp123]

Have you got good assemblies? The wrong peak_hom will affect the overlap calculation, as hifiasm will check up to peak_hom*(-D) overlaps for each read during correction. It seems that --hg-size did not work as the k-mer plot is a little bit weird. So probably the only solution is to double the option -D.

[chhylp123]

You may also need to set --hom-cov to 50. Please note this option only affects the graph cleaning step.

[amit4mchiba]

Thank you so much for your reply. Following your advice, I firstly used subreads and performed the extraction of Hifi reads by firstly running ccs and then extracthifi for all the reads. The idea here was to get same processing in order to remove any unspecific error. Next, I run hifiasm using default parameters (please see below)- (base) amit8riken@amit8riken:/mnt/HD2/HiFi_data/HiFi_reads$ hifiasm -o Nfoetida_hifi-1.asm -s 0.5 -t48 -f38 -D9 --hg-size 9800m --max-kocc 6000 -a6 .fasta.gz [M::ha_analyze_count] lowest: count[5] = 42085295 [M::ha_analyze_count] highest: count[46] = 108614532 [M::ha_hist_line] 2: ****************************************************************************************** 98171527 [M::ha_hist_line] 3: ****************************************** 45894072 [M::ha_hist_line] 4: *************************************** 42133006 [M::ha_hist_line] 5: *************************************** 42085295 [M::ha_hist_line] 6: **************************************** 43707228 [M::ha_hist_line] 7: ******************************************* 46839737 [M::ha_hist_line] 8: ********************************************** 50052218 [M::ha_hist_line] 9: ************************************************ 52500806 [M::ha_hist_line] 10: ************************************************* 53288502 [M::ha_hist_line] 11: ************************************************* 52994107 [M::ha_hist_line] 12: ************************************************ 51689951 [M::ha_hist_line] 13: ********************************************** 49913249 [M::ha_hist_line] 14: ******************************************** 48312244 [M::ha_hist_line] 15: ******************************************* 47170344 [M::ha_hist_line] 16: ******************************************* 46404573 [M::ha_hist_line] 17: ******************************************* 46293705 [M::ha_hist_line] 18: ******************************************* 46407005 [M::ha_hist_line] 19: ******************************************* 46820245 [M::ha_hist_line] 20: ******************************************* 47165040 [M::ha_hist_line] 21: ******************************************* 47160801 [M::ha_hist_line] 22: ******************************************* 47101601 [M::ha_hist_line] 23: ******************************************* 46651876 [M::ha_hist_line] 24: ******************************************* 46213302 [M::ha_hist_line] 25: ****************************************** 45717124 [M::ha_hist_line] 26: ****************************************** 45494768 [M::ha_hist_line] 27: ****************************************** 45610065 [M::ha_hist_line] 28: ******************************************* 46193641 [M::ha_hist_line] 29: ******************************************** 47407291 [M::ha_hist_line] 30: ********************************************* 49337267 [M::ha_hist_line] 31: ************************************************ 51632308 [M::ha_hist_line] 32: *************************************************** 54859803 [M::ha_hist_line] 33: ****************************************************** 58665751 [M::ha_hist_line] 34: ********************************************************** 63107192 [M::ha_hist_line] 35: ************************************************************** 67838471 [M::ha_hist_line] 36: ******************************************************************* 72947192 [M::ha_hist_line] 37: ************************************************************************ 78071856 [M::ha_hist_line] 38: ***************************************************************************** 83295035 [M::ha_hist_line] 39: ********************************************************************************* 88357982 [M::ha_hist_line] 40: ************************************************************************************** 92899721 [M::ha_hist_line] 41: ***************************************************************************************** 97079963 [M::ha_hist_line] 42: ********************************************************************************************* 100867479 [M::ha_hist_line] 43: ************************************************************************************************ 104000539 [M::ha_hist_line] 44: ************************************************************************************************** 106373443 [M::ha_hist_line] 45: *************************************************************************************************** 107812736 [M::ha_hist_line] 46: **************************************************************************************************** 108614532 [M::ha_hist_line] 47: **************************************************************************************************** 108586105 [M::ha_hist_line] 48: *************************************************************************************************** 107819561 [M::ha_hist_line] 49: ************************************************************************************************** 106150013 [M::ha_hist_line] 50: ************************************************************************************************ 103799849 [M::ha_hist_line] 51: ********************************************************************************************* 100702188 [M::ha_hist_line] 52: ***************************************************************************************** 96769637 [M::ha_hist_line] 53: ************************************************************************************* 92376769 [M::ha_hist_line] 54: ********************************************************************************* 87474282 [M::ha_hist_line] 55: **************************************************************************** 82177951 [M::ha_hist_line] 56: ********************************************************************** 76567973 [M::ha_hist_line] 57: ***************************************************************** 70464938 [M::ha_hist_line] 58: *********************************************************** 64311587 [M::ha_hist_line] 59: ****************************************************** 58112489 [M::ha_hist_line] 60: ************************************************ 52151919 [M::ha_hist_line] 61: ******************************************* 46360018 [M::ha_hist_line] 62: ************************************** 40786206 [M::ha_hist_line] 63: ********************************* 35544163 [M::ha_hist_line] 64: **************************** 30703639 [M::ha_hist_line] 65: ************************ 26335389 [M::ha_hist_line] 66: ********************* 22329567 [M::ha_hist_line] 67: ***************** 18863139 [M::ha_hist_line] 68: *************** 15782212 [M::ha_hist_line] 69: ************ 13110247 [M::ha_hist_line] 70: ********** 10870426 [M::ha_hist_line] 71: ******** 8978193 [M::ha_hist_line] 72: ******* 7371624 [M::ha_hist_line] 73: ****** 6078253 [M::ha_hist_line] 74: ***** 5025647 [M::ha_hist_line] 75: **** 4135879 [M::ha_hist_line] 76: *** 3436673 [M::ha_hist_line] 77: *** 2899437 [M::ha_hist_line] 78: ** 2479454 [M::ha_hist_line] 79: ** 2164986 [M::ha_hist_line] 80: ** 1933537 [M::ha_hist_line] 81: ** 1760651 [M::ha_hist_line] 82: * 1630116 [M::ha_hist_line] 83: * 1534145 [M::ha_hist_line] 84: * 1462672 [M::ha_hist_line] 85: * 1403166 [M::ha_hist_line] 86: * 1359774 [M::ha_hist_line] 87: * 1337132 [M::ha_hist_line] 88: * 1307044 [M::ha_hist_line] 89: * 1305431 [M::ha_hist_line] 90: * 1298228 [M::ha_hist_line] 91: * 1284346 [M::ha_hist_line] 92: * 1266844 [M::ha_hist_line] 93: * 1256364 [M::ha_hist_line] 94: * 1243643 [M::ha_hist_line] 95: * 1231871 [M::ha_hist_line] 96: * 1210381 [M::ha_hist_line] 97: * 1197973 [M::ha_hist_line] 98: * 1179923 [M::ha_hist_line] 99: * 1165340 [M::ha_hist_line] 100: * 1145178 [M::ha_hist_line] 101: * 1128623 [M::ha_hist_line] 102: * 1112425 [M::ha_hist_line] 103: * 1095435 [M::ha_hist_line] 104: * 1064785 [M::ha_hist_line] 105: * 1037998 [M::ha_hist_line] 106: * 1014340 [M::ha_hist_line] 107: * 983427 [M::ha_hist_line] 108: * 954853 [M::ha_hist_line] 109: * 920449 [M::ha_hist_line] 110: * 888031 [M::ha_hist_line] 111: * 864545 [M::ha_hist_line] 112: * 834205 [M::ha_hist_line] 113: * 799574 [M::ha_hist_line] 114: * 773955 [M::ha_hist_line] 115: * 744179 [M::ha_hist_line] 116: * 712406 [M::ha_hist_line] 117: * 683610 [M::ha_hist_line] 118: * 652467 [M::ha_hist_line] 119: * 620146 [M::ha_hist_line] 120: * 598869 [M::ha_hist_line] 121: * 565326 [M::ha_hist_line] rest: ******************************* 33423555 [M::ha_analyze_count] left: count[10] = 53288502 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 27; peak_het: 10 [M::ha_ct_shrink::11001.60412.59] ==> counted 11620250 distinct minimizer k-mers [M::ha_ft_gen::11029.881[email protected]] ==> filtered out 11620250 k-mers occurring 243 or more times [M::ha_opt_update_cov] updated max_n_chain to 243 [M::yak_count] collected 1167222785 minimizers [M::yak_count] collected 988060897 minimizers [M::yak_count] collected 445761699 minimizers [M::yak_count] collected 221584481 minimizers [M::yak_count] collected 114937260 minimizers [M::yak_count] collected 144405250 minimizers [M::yak_count] collected 121494660 minimizers [M::yak_count] collected 126994859 minimizers [M::yak_count] collected 225446080 minimizers [M::yak_count] collected 210310208 minimizers [M::yak_count] collected 334434440 minimizers [M::yak_count] collected 316868390 minimizers [M::yak_count] collected 265488901 minimizers [M::yak_count] collected 140989660 minimizers [M::yak_count] collected 404628283 minimizers [M::yak_count] collected 749783299 minimizers [M::yak_count] collected 428374952 minimizers [M::yak_count] collected 493410726 minimizers [M::yak_count] collected 325272864 minimizers [M::ha_pt_gen::14564.37313.03] ==> counted 376437377 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 2170421 [M::ha_analyze_count] highest: count[46] = 4378528 [M::ha_hist_line] 1: ****************************************************************************************************> 185676595 [M::ha_hist_line] 2: ************************************************************************************************> 7605762 [M::ha_hist_line] 3: ******************************************************************* 2916038 [M::ha_hist_line] 4: **************************************************** 2286111 [M::ha_hist_line] 5: ************************************************** 2170421 [M::ha_hist_line] 6: ************************************************** 2208398 [M::ha_hist_line] 7: ***************************************************** 2331990 [M::ha_hist_line] 8: ******************************************************** 2460916 [M::ha_hist_line] 9: *********************************************************** 2561702 [M::ha_hist_line] 10: *********************************************************** 2582337 [M::ha_hist_line] 11: ********************************************************** 2550644 [M::ha_hist_line] 12: ********************************************************* 2476717 [M::ha_hist_line] 13: ****************************************************** 2381462 [M::ha_hist_line] 14: **************************************************** 2297271 [M::ha_hist_line] 15: *************************************************** 2232119 [M::ha_hist_line] 16: ************************************************** 2182068 [M::ha_hist_line] 17: ************************************************* 2164333 [M::ha_hist_line] 18: ************************************************* 2154727 [M::ha_hist_line] 19: ************************************************* 2162852 [M::ha_hist_line] 20: ************************************************* 2164029 [M::ha_hist_line] 21: ************************************************* 2158377 [M::ha_hist_line] 22: ************************************************* 2146242 [M::ha_hist_line] 23: ************************************************ 2119957 [M::ha_hist_line] 24: ************************************************ 2097584 [M::ha_hist_line] 25: *********************************************** 2074003 [M::ha_hist_line] 26: *********************************************** 2060845 [M::ha_hist_line] 27: *********************************************** 2061871 [M::ha_hist_line] 28: ************************************************ 2082408 [M::ha_hist_line] 29: ************************************************* 2129154 [M::ha_hist_line] 30: ************************************************** 2199789 [M::ha_hist_line] 31: **************************************************** 2290784 [M::ha_hist_line] 32: ******************************************************* 2413707 [M::ha_hist_line] 33: ********************************************************** 2561404 [M::ha_hist_line] 34: ************************************************************** 2727791 [M::ha_hist_line] 35: ****************************************************************** 2907850 [M::ha_hist_line] 36: *********************************************************************** 3098912 [M::ha_hist_line] 37: *************************************************************************** 3291409 [M::ha_hist_line] 38: ******************************************************************************** 3486117 [M::ha_hist_line] 39: ************************************************************************************ 3671766 [M::ha_hist_line] 40: **************************************************************************************** 3837527 [M::ha_hist_line] 41: ******************************************************************************************* 3990050 [M::ha_hist_line] 42: ********************************************************************************************** 4124861 [M::ha_hist_line] 43: ************************************************************************************************* 4229606 [M::ha_hist_line] 44: *************************************************************************************************** 4315071 [M::ha_hist_line] 45: *************************************************************************************************** 4356678 [M::ha_hist_line] 46: **************************************************************************************************** 4378528 [M::ha_hist_line] 47: **************************************************************************************************** 4364269 [M::ha_hist_line] 48: *************************************************************************************************** 4319437 [M::ha_hist_line] 49: ************************************************************************************************* 4247745 [M::ha_hist_line] 50: *********************************************************************************************** 4145609 [M::ha_hist_line] 51: ******************************************************************************************** 4011859 [M::ha_hist_line] 52: **************************************************************************************** 3850162 [M::ha_hist_line] 53: ************************************************************************************ 3667055 [M::ha_hist_line] 102: * 62972 [M::ha_hist_line] 103: * 62302 [M::ha_hist_line] 104: * 60883 [M::ha_hist_line] 105: * 59564 [M::ha_hist_line] 106: * 58714 [M::ha_hist_line] 107: * 56590 [M::ha_hist_line] 108: * 55264 [M::ha_hist_line] 109: * 53323 [M::ha_hist_line] 110: * 52151 [M::ha_hist_line] 111: * 51017 [M::ha_hist_line] 112: * 49296 [M::ha_hist_line] 113: * 47191 [M::ha_hist_line] 114: * 45835 [M::ha_hist_line] 115: * 44244 [M::ha_hist_line] 116: * 42708 [M::ha_hist_line] 117: * 40974 [M::ha_hist_line] 118: * 39520 [M::ha_hist_line] 119: * 37789 [M::ha_hist_line] 120: * 36338 [M::ha_hist_line] 121: * 34942 [M::ha_hist_line] 122: * 33699 [M::ha_hist_line] 123: * 32040 [M::ha_hist_line] 124: * 30784 [M::ha_hist_line] 125: * 29332 [M::ha_hist_line] 126: * 28048 [M::ha_hist_line] 127: * 27778 [M::ha_hist_line] 128: * 26157 [M::ha_hist_line] 129: * 25591 [M::ha_hist_line] 130: * 24550 [M::ha_hist_line] 131: * 24181 [M::ha_hist_line] 132: * 22935 [M::ha_hist_line] 133: * 22488 [M::ha_hist_line] rest: ************************** 1122152 [M::ha_analyze_count] left: count[10] = 2582337 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 27; peak_het: 10 [M::ha_ct_shrink::14565.77013.03] ==> counted 190760782 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7225469694 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::16805.86714.59] ==> indexed 7039793099 positions, counted 190760782 distinct minimizer k-mers [M::ha_assemble::60235.267[email protected]] ==> corrected reads for round 1 [M::ha_assemble] # bases: 268025297616; # corrected bases: 732329153; # recorrected bases: 491067 [M::ha_assemble] size of buffer: 89.421GB [M::yak_count] collected 7214162232 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::62264.89130.85] ==> counted 213499902 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 1897540 [M::ha_analyze_count] highest: count[47] = 4301716 [M::ha_hist_line] 1: ************************************************************************************************> 30652284 [M::ha_hist_line] 2: ******************************************** 1899145 [M::ha_hist_line] 3: **************************************** 1718468 [M::ha_hist_line] 4: ****************************************** 1825261 [M::ha_hist_line] 5: ******************************************** 1897540 [M::ha_hist_line] 6: *********************************************** 2010293 [M::ha_hist_line] 7: ************************************************** 2168701 [M::ha_hist_line] 8: ****************************************************** 2315106 [M::ha_hist_line] 105: * 61314 [M::ha_hist_line] 106: * 59863 [M::ha_hist_line] 107: * 58593 [M::ha_hist_line] 108: * 57603 [M::ha_hist_line] 109: * 56147 [M::ha_hist_line] 110: * 54533 [M::ha_hist_line] 111: * 53218 [M::ha_hist_line] 112: * 51999 [M::ha_hist_line] 113: * 50660 [M::ha_hist_line] 114: * 49186 [M::ha_hist_line] 115: * 46985 [M::ha_hist_line] 116: * 45744 [M::ha_hist_line] 117: * 44892 [M::ha_hist_line] 118: * 42412 [M::ha_hist_line] 119: * 41279 [M::ha_hist_line] 120: * 39484 [M::ha_hist_line] 121: * 37890 [M::ha_hist_line] 122: * 36117 [M::ha_hist_line] 123: * 35395 [M::ha_hist_line] 124: * 33523 [M::ha_hist_line] 125: * 32251 [M::ha_hist_line] 126: * 30791 [M::ha_hist_line] 127: * 29765 [M::ha_hist_line] 128: * 28423 [M::ha_hist_line] 129: * 27872 [M::ha_hist_line] 130: * 26466 [M::ha_hist_line] 131: * 25482 [M::ha_hist_line] 132: * 24670 [M::ha_hist_line] 133: * 23842 [M::ha_hist_line] 134: * 23444 [M::ha_hist_line] 135: * 22667 [M::ha_hist_line] 136: * 21791 [M::ha_hist_line] rest: ************************** 1117804 [M::ha_analyze_count] left: count[10] = 2485031 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 27; peak_het: 10 [M::ha_ct_shrink::62265.85130.85] ==> counted 182847618 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7214162232 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::64452.08730.60] ==> indexed 7183509948 positions, counted 182847618 distinct minimizer k-mers [M::ha_assemble::104153.875[email protected]] ==> corrected reads for round 2 [M::ha_assemble] # bases: 267879878336; # corrected bases: 71294075; # recorrected bases: 118268 [M::ha_assemble] size of buffer: 91.198GB [M::yak_count] collected 7212229781 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::106255.83733.07] ==> counted 193347847 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 1864750 [M::ha_analyze_count] highest: count[48] = 4296753 [M::ha_hist_line] 1: ************************************************************************************************> 11129709 [M::ha_hist_line] 2: ************************************ 1550118 [M::ha_hist_line] 3: ************************************ 1543743 [M::ha_hist_line] 4: ***************************************** 1769477 [M::ha_hist_line] 5: ******************************************* 1864750 [M::ha_hist_line] 6: ********************************************** 1991324 [M::ha_hist_line] 7: ************************************************** 2153512 [M::ha_hist_line] 8: ****************************************************** 2303333 [M::ha_hist_line] 9: ******************************************************** 2427547 [M::ha_hist_line] 10: ********************************************************** 2477171 [M::ha_hist_line] 11: ********************************************************* 2466667 [M::ha_hist_line] 12: ******************************************************** 2414642 [M::ha_hist_line] 13: ****************************************************** 2324440 [M::ha_hist_line] 14: **************************************************** 2240489 [M::ha_hist_line] 15: *************************************************** 2178371 [M::ha_hist_line] 16: ************************************************* 2120159 [M::ha_hist_line] 17: ************************************************* 2094184 [M::ha_hist_line] 18: ************************************************* 2084250 [M::ha_hist_line] 19: ************************************************* 2084614 [M::ha_hist_line] 20: ************************************************* 2097488 [M::ha_hist_line] 21: ************************************************* 2096794 [M::ha_hist_line] 22: ************************************************* 2092540 [M::ha_hist_line] 23: ************************************************ 2074013 [M::ha_hist_line] 24: ************************************************ 2051191 [M::ha_hist_line] 25: *********************************************** 2024153 [M::ha_hist_line] 26: *********************************************** 2006275 [M::ha_hist_line] 27: *********************************************** 1998296 [M::ha_hist_line] 28: *********************************************** 1998195 [M::ha_hist_line] 29: *********************************************** 2017368 [M::ha_hist_line] 30: ************************************************ 2072970 [M::ha_hist_line] 31: ************************************************** 2132108 [M::ha_hist_line] 32: **************************************************** 2230554 [M::ha_hist_line] 33: ******************************************************* 2348695 [M::ha_hist_line] 34: ********************************************************** 2491478 [M::ha_hist_line] 35: ************************************************************** 2656026 [M::ha_hist_line] 36: ****************************************************************** 2826519 [M::ha_hist_line] 37: ********************************************************************** 3012752 [M::ha_hist_line] 38: *************************************************************************** 3203708 [M::ha_hist_line] 39: ******************************************************************************* 3383212 [M::ha_hist_line] 40: *********************************************************************************** 3571308 [M::ha_hist_line] 41: *************************************************************************************** 3735720 [M::ha_hist_line] 42: ****************************************************************************************** 3880842 [M::ha_hist_line] 43: ********************************************************************************************** 4027172 [M::ha_hist_line] 44: ************************************************************************************************ 4134533 [M::ha_hist_line] 45: ************************************************************************************************** 4216754 [M::ha_hist_line] 46: *************************************************************************************************** 4265069 [M::ha_hist_line] 47: **************************************************************************************************** 4294435 [M::ha_hist_line] 48: **************************************************************************************************** 4296753 [M::ha_hist_line] 49: *************************************************************************************************** 4258363 [M::ha_hist_line] 50: ************************************************************************************************** 4198482 [M::ha_hist_line] 51: ************************************************************************************************ 4111232 [M::ha_hist_line] 52: ********************************************************************************************* 3995397 [M::ha_hist_line] 53: ***************************************************************************************** 3844540 [M::ha_hist_line] 54: ************************************************************************************* 3673683 [M::ha_hist_line] 55: ********************************************************************************* 3483756 [M::ha_hist_line] 56: **************************************************************************** 3286686 [M::ha_hist_line] 57: ************************************************************************ 3074319 [M::ha_hist_line] 58: ****************************************************************** 2835290 [M::ha_hist_line] 59: ************************************************************ 2590743 [M::ha_hist_line] 60: ******************************************************* 2359929 [M::ha_hist_line] 61: ************************************************* 2122354 [M::ha_hist_line] 62: ******************************************** 1900102 [M::ha_hist_line] 63: *************************************** 1679412 [M::ha_hist_line] 64: ********************************** 1471294 [M::ha_hist_line] 65: ****************************** 1280098 [M::ha_hist_line] 66: ************************** 1103537 [M::ha_hist_line] 67: ********************** 946084 [M::ha_hist_line] 68: ******************* 806272 [M::ha_hist_line] 69: **************** 680523 [M::ha_hist_line] 70: ************* 571901 [M::ha_hist_line] 71: *********** 477921 [M::ha_hist_line] 72: ********* 400352 [M::ha_hist_line] 73: ******** 332563 [M::ha_hist_line] 74: ****** 277640 [M::ha_hist_line] 75: ***** 236019 [M::ha_hist_line] 76: ***** 197557 [M::ha_hist_line] 77: **** 169053 [M::ha_hist_line] 78: *** 143133 [M::ha_hist_line] 79: *** 125408 [M::ha_hist_line] 80: *** 111259 [M::ha_hist_line] 81: ** 100595 [M::ha_hist_line] 82: ** 92910 [M::ha_hist_line] 83: ** 86673 [M::ha_hist_line] 84: ** 82959 [M::ha_hist_line] 85: ** 78857 [M::ha_hist_line] 86: ** 76607 [M::ha_hist_line] 87: ** 73393 [M::ha_hist_line] 88: ** 72695 [M::ha_hist_line] 89: ** 72056 [M::ha_hist_line] 90: ** 71486 [M::ha_hist_line] 91: ** 70503 [M::ha_hist_line] 92: ** 69420 [M::ha_hist_line] 93: ** 69280 [M::ha_hist_line] 94: ** 68415 [M::ha_hist_line] 95: ** 68744 [M::ha_hist_line] 96: ** 67909 [M::ha_hist_line] 97: ** 67045 [M::ha_hist_line] 98: ** 66432 [M::ha_hist_line] 99: ** 65796 [M::ha_hist_line] 100: ** 65265 [M::ha_hist_line] 101: * 64209 [M::ha_hist_line] 102: * 64077 [M::ha_hist_line] 103: * 62669 [M::ha_hist_line] 104: * 61796 [M::ha_hist_line] 105: * 61566 [M::ha_hist_line] 106: * 60337 [M::ha_hist_line] 107: * 59029 [M::ha_hist_line] 108: * 57653 [M::ha_hist_line] 109: * 56086 [M::ha_hist_line] 110: * 55006 [M::ha_hist_line] 111: * 53482 [M::ha_hist_line] 112: * 51617 [M::ha_hist_line] 113: * 51082 [M::ha_hist_line] 114: * 49681 [M::ha_hist_line] 115: * 47377 [M::ha_hist_line] 116: * 46450 [M::ha_hist_line] 117: * 44937 [M::ha_hist_line] 118: * 42773 [M::ha_hist_line] 119: * 41870 [M::ha_hist_line] 120: * 39716 [M::ha_hist_line] 121: * 38230 [M::ha_hist_line] 122: * 36485 [M::ha_hist_line] 123: * 35681 [M::ha_hist_line] 124: * 33929 [M::ha_hist_line] 125: * 32576 [M::ha_hist_line] 126: * 30826 [M::ha_hist_line] 127: * 30048 [M::ha_hist_line] 128: * 28491 [M::ha_hist_line] 129: * 28030 [M::ha_hist_line] 130: * 26986 [M::ha_hist_line] 131: * 25491 [M::ha_hist_line] 132: * 25231 [M::ha_hist_line] 133: * 23872 [M::ha_hist_line] 134: * 23318 [M::ha_hist_line] 135: * 22741 [M::ha_hist_line] 136: * 22019 [M::ha_hist_line] rest: ************************** 1125117 [M::ha_analyze_count] left: count[10] = 2477171 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 27; peak_het: 10 [M::ha_ct_shrink::106256.23433.07] ==> counted 182218138 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7212229781 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::108771.72132.80] ==> indexed 7201100072 positions, counted 182218138 distinct minimizer k-mers [M::ha_assemble::148170.635[email protected]] ==> corrected reads for round 3 [M::ha_assemble] # bases: 267866286696; # corrected bases: 7090258; # recorrected bases: 119243 [M::ha_assemble] size of buffer: 90.483GB [M::yak_count] collected 7211573249 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::150254.46433.94] ==> counted 191381000 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 1855997 [M::ha_analyze_count] highest: count[48] = 4297929 [M::ha_hist_line] 1: **************************************************************************************************> 9348193 [M::ha_hist_line] 2: ********************************** 1465532 [M::ha_hist_line] 3: *********************************** 1486351 [M::ha_hist_line] 4: ***************************************** 1755518 [M::ha_hist_line] 5: ******************************************* 1855997 [M::ha_hist_line] 6: ********************************************** 1985712 [M::ha_hist_line] 7: ************************************************** 2149996 [M::ha_hist_line] 8: ****************************************************** 2300217 [M::ha_hist_line] 9: ******************************************************** 2425351 [M::ha_hist_line] 10: ********************************************************** 2475029 [M::ha_hist_line] 11: ********************************************************* 2464576 [M::ha_hist_line] 12: ******************************************************** 2413224 [M::ha_hist_line] 13: ****************************************************** 2323013 [M::ha_hist_line] 14: **************************************************** 2239074 [M::ha_hist_line] 15: *************************************************** 2176839 [M::ha_hist_line] 16: ************************************************* 2119286 [M::ha_hist_line] 17: ************************************************* 2092781 [M::ha_hist_line] 18: ************************************************ 2083504 [M::ha_hist_line] 19: ************************************************ 2083098 [M::ha_hist_line] 20: ************************************************* 2096993 [M::ha_hist_line] 21: ************************************************* 2095663 [M::ha_hist_line] 22: ************************************************* 2091219 [M::ha_hist_line] 23: ************************************************ 2073350 [M::ha_hist_line] 24: ************************************************ 2050452 [M::ha_hist_line] 25: *********************************************** 2023592 [M::ha_hist_line] 26: *********************************************** 2004672 [M::ha_hist_line] 27: ********************************************** 1996734 [M::ha_hist_line] 28: ********************************************** 1997123 [M::ha_hist_line] 29: *********************************************** 2016387 [M::ha_hist_line] 30: ************************************************ 2071558 [M::ha_hist_line] 31: ************************************************** 2130345 [M::ha_hist_line] 32: **************************************************** 2228701 [M::ha_hist_line] 33: ******************************************************* 2345613 [M::ha_hist_line] 34: ********************************************************** 2488532 [M::ha_hist_line] 35: ************************************************************** 2653166 [M::ha_hist_line] 36: ****************************************************************** 2824667 [M::ha_hist_line] 37: ********************************************************************** 3009996 [M::ha_hist_line] 38: ************************************************************************** 3200953 [M::ha_hist_line] 39: ******************************************************************************* 3380823 [M::ha_hist_line] 40: *********************************************************************************** 3569336 [M::ha_hist_line] 41: *************************************************************************************** 3733555 [M::ha_hist_line] 42: ****************************************************************************************** 3879325 [M::ha_hist_line] 43: ********************************************************************************************** 4025126 [M::ha_hist_line] 44: ************************************************************************************************ 4132966 [M::ha_hist_line] 45: ************************************************************************************************** 4216197 [M::ha_hist_line] 46: *************************************************************************************************** 4266109 [M::ha_hist_line] 47: **************************************************************************************************** 4293155 [M::ha_hist_line] 48: **************************************************************************************************** 4297929 [M::ha_hist_line] 49: *************************************************************************************************** 4257794 [M::ha_hist_line] 50: ************************************************************************************************** 4200022 [M::ha_hist_line] 51: ************************************************************************************************ 4111842 [M::ha_hist_line] 52: ********************************************************************************************* 3996462 [M::ha_hist_line] 53: ****************************************************************************************** 3847534 [M::ha_hist_line] 54: ************************************************************************************** 3675896 [M::ha_hist_line] 55: ********************************************************************************* 3486250 [M::ha_hist_line] 56: ***************************************************************************** 3288893 [M::ha_hist_line] 57: ************************************************************************ 3077065 [M::ha_hist_line] 58: ****************************************************************** 2838114 [M::ha_hist_line] 59: ************************************************************ 2593925 [M::ha_hist_line] 60: ******************************************************* 2362622 [M::ha_hist_line] 61: ************************************************* 2124870 [M::ha_hist_line] 62: ******************************************** 1903352 [M::ha_hist_line] 63: *************************************** 1681416 [M::ha_hist_line] 64: ********************************** 1474011 [M::ha_hist_line] 65: ****************************** 1282583 [M::ha_hist_line] 66: ************************** 1104842 [M::ha_hist_line] 67: ********************** 948256 [M::ha_hist_line] 68: ******************* 807702 [M::ha_hist_line] 69: **************** 682528 [M::ha_hist_line] 70: ************* 572907 [M::ha_hist_line] 71: *********** 478812 [M::ha_hist_line] 72: ********* 401390 [M::ha_hist_line] 73: ******** 332827 [M::ha_hist_line] 74: ****** 278488 [M::ha_hist_line] 75: ****** 236471 [M::ha_hist_line] 76: ***** 197895 [M::ha_hist_line] 77: **** 169250 [M::ha_hist_line] 78: *** 143402 [M::ha_hist_line] 79: *** 125502 [M::ha_hist_line] 80: *** 111399 [M::ha_hist_line] 81: ** 100707 [M::ha_hist_line] 82: ** 92903 [M::ha_hist_line] 83: ** 86736 [M::ha_hist_line] 84: ** 82818 [M::ha_hist_line] 85: ** 79049 [M::ha_hist_line] 86: ** 76596 [M::ha_hist_line] 87: ** 73414 [M::ha_hist_line] 88: ** 72786 [M::ha_hist_line] 89: ** 72078 [M::ha_hist_line] 90: ** 71473 [M::ha_hist_line] 91: ** 70378 [M::ha_hist_line] 92: ** 69435 [M::ha_hist_line] 93: ** 69251 [M::ha_hist_line] 94: ** 68381 [M::ha_hist_line] 95: ** 68718 [M::ha_hist_line] 96: ** 67948 [M::ha_hist_line] 97: ** 67034 [M::ha_hist_line] 98: ** 66492 [M::ha_hist_line] 99: ** 65684 [M::ha_hist_line] 100: ** 65360 [M::ha_hist_line] 101: * 64283 [M::ha_hist_line] 102: * 64018 [M::ha_hist_line] 103: * 62682 [M::ha_hist_line] 104: * 61848 [M::ha_hist_line] 105: * 61432 [M::ha_hist_line] 106: * 60400 [M::ha_hist_line] 107: * 59096 [M::ha_hist_line] 108: * 57781 [M::ha_hist_line] 109: * 56065 [M::ha_hist_line] 110: * 55039 [M::ha_hist_line] 111: * 53559 [M::ha_hist_line] 112: * 51528 [M::ha_hist_line] 113: * 51102 [M::ha_hist_line] 114: * 49732 [M::ha_hist_line] 115: * 47480 [M::ha_hist_line] 116: * 46389 [M::ha_hist_line] 117: * 45048 [M::ha_hist_line] 118: * 42834 [M::ha_hist_line] 119: * 41754 [M::ha_hist_line] 120: * 39749 [M::ha_hist_line] 121: * 38253 [M::ha_hist_line] 122: * 36600 [M::ha_hist_line] 123: * 35691 [M::ha_hist_line] 124: * 33880 [M::ha_hist_line] 125: * 32626 [M::ha_hist_line] 126: * 30845 [M::ha_hist_line] 127: * 30093 [M::ha_hist_line] 128: * 28491 [M::ha_hist_line] 129: * 28079 [M::ha_hist_line] 130: * 26904 [M::ha_hist_line] 131: * 25498 [M::ha_hist_line] 132: * 25370 [M::ha_hist_line] 133: * 23854 [M::ha_hist_line] 134: * 23301 [M::ha_hist_line] 135: * 22719 [M::ha_hist_line] 136: * 21984 [M::ha_hist_line] rest: ************************** 1125902 [M::ha_analyze_count] left: count[10] = 2475029 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 27; peak_het: 10 [M::ha_ct_shrink::150254.96633.94] ==> counted 182032807 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 7211573249 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::yak_count] collected 0 minimizers [M::ha_pt_gen::152477.90333.80] ==> indexed 7202225056 positions, counted 182032807 distinct minimizer k-mers

The histogram looks very strange to me as you can see that for the last one, there are two peaks, and then a kind of horizontal area. I am not sure if this is a problem or what. Also, it seems that the default parameters seems taking wrong peak_hom, which might be the reason for the bad assembly. Before start re-run the program, I was curious about the histogram itself and if There is something I need to feel worried about? Do you feel that it could have some contamination? All sequencing were done using same plant tissue, nevertheless, this is what I am getting it here. Based on the histogram, I felt that the genome is relatively more homozygous, isn't it?

I am looking forward to hear your opinion. Please advise me if I should re-run the program with the same dataset or if there is some specific parameter that I should use to manage this nature of histogram?

thank you so much,

with best regards Amit

[amit4mchiba]

Goodmorning from Japan.

I started re-running HiFIASM, and although it is not over yet, the first kmer plot seems like this (command used were-hifiasm -o Nfoetida_hifi_vaishu3.asm -s 0.5 -t48 -f39 -D18 -N120 -r5 --hom-cov 50 --hg-size 10g --max-kocc 6000 *.hifi_reads.fasta.gz) What's interesting here is that I can see three peaks, at 10, 21, and 52. What does this mean? I do understand the concept of homozygous and heterozygous peaks, but then three peaks are a little strange, isn't it? I have not done karyotyping for my plant yet, but based on publications, it is a diploid plant. Please advice me.

run_hifiasm-vaishu3.sh: line 2: $'\r': command not found [M::ha_analyze_count] lowest: count[5] = 41809256 [M::ha_analyze_count] highest: count[52] = 103146417 [M::ha_hist_line] 2: *************************************************************************************************> 108447537 [M::ha_hist_line] 3: ********************************************* 46221277 [M::ha_hist_line] 4: ***************************************** 42200932 [M::ha_hist_line] 5: ***************************************** 41809256 [M::ha_hist_line] 6: ***************************************** 42535417 [M::ha_hist_line] 7: ******************************************* 44214410 [M::ha_hist_line] 8: ********************************************* 46215152 [M::ha_hist_line] 9: ********************************************** 47747033 [M::ha_hist_line] 10: *********************************************** 48104334 [M::ha_hist_line] 11: ********************************************** 47442692 [M::ha_hist_line] 12: ********************************************* 46207521 [M::ha_hist_line] 13: ******************************************* 44569714 [M::ha_hist_line] 14: ****************************************** 43390374 [M::ha_hist_line] 15: ***************************************** 42555267 [M::ha_hist_line] 16: ***************************************** 42256585 [M::ha_hist_line] 17: ***************************************** 42547082 [M::ha_hist_line] 18: ****************************************** 43068313 [M::ha_hist_line] 19: ****************************************** 43654542 [M::ha_hist_line] 20: ******************************************* 44141044 [M::ha_hist_line] 21: ******************************************* 44064847 [M::ha_hist_line] 22: ****************************************** 43721239 [M::ha_hist_line] 23: ****************************************** 42928688 [M::ha_hist_line] 24: ***************************************** 41884444 [M::ha_hist_line] 25: *************************************** 40659046 [M::ha_hist_line] 26: ************************************** 39518301 [M::ha_hist_line] 27: ************************************* 38423631 [M::ha_hist_line] 28: ************************************ 37493530 [M::ha_hist_line] 29: ************************************ 36968190 [M::ha_hist_line] 30: ************************************ 37043327 [M::ha_hist_line] 31: ************************************ 37468350 [M::ha_hist_line] 32: ************************************* 38392505 [M::ha_hist_line] 33: *************************************** 39830428 [M::ha_hist_line] 34: **************************************** 41751464 [M::ha_hist_line] 35: ******************************************* 44134610 [M::ha_hist_line] 36: ********************************************** 47046864 [M::ha_hist_line] 37: ************************************************* 50440275 [M::ha_hist_line] 38: ***************************************************** 54220973 [M::ha_hist_line] 39: ********************************************************* 58432646 [M::ha_hist_line] 40: ************************************************************* 62979042 [M::ha_hist_line] 41: ****************************************************************** 67845232 [M::ha_hist_line] 42: ********************************************************************** 72677251 [M::ha_hist_line] 43: *************************************************************************** 77424098 [M::ha_hist_line] 44: ******************************************************************************** 82032851 [M::ha_hist_line] 45: ************************************************************************************ 86425374 [M::ha_hist_line] 46: **************************************************************************************** 90616632 [M::ha_hist_line] 47: ******************************************************************************************** 94430474 [M::ha_hist_line] 48: *********************************************************************************************** 97507164 [M::ha_hist_line] 49: ************************************************************************************************* 100000754 [M::ha_hist_line] 50: *************************************************************************************************** 101632015 [M::ha_hist_line] 51: *************************************************************************************************** 102621063 [M::ha_hist_line] 52: **************************************************************************************************** 103146417 [M::ha_hist_line] 53: **************************************************************************************************** 102853861 [M::ha_hist_line] 54: *************************************************************************************************** 101789230 [M::ha_hist_line] 55: ************************************************************************************************* 100059062 [M::ha_hist_line] 56: *********************************************************************************************** 97560245 [M::ha_hist_line] 57: ******************************************************************************************** 94424301 [M::ha_hist_line] 58: **************************************************************************************** 90655371 [M::ha_hist_line] 59: ************************************************************************************ 86412823 [M::ha_hist_line] 60: ******************************************************************************* 81829882 [M::ha_hist_line] 61: ************************************************************************** 76786577 [M::ha_hist_line] 62: ********************************************************************* 71411564 [M::ha_hist_line] 63: **************************************************************** 66003707 [M::ha_hist_line] 64: ********************************************************** 60291008 [M::ha_hist_line] 65: ***************************************************** 54720802 [M::ha_hist_line] 66: ************************************************ 49176888 [M::ha_hist_line] 67: ****************************************** 43814088 [M::ha_hist_line] 68: ************************************** 38800279 [M::ha_hist_line] 69: ********************************* 34015664 [M::ha_hist_line] 70: ***************************** 29564885 [M::ha_hist_line] 71: ************************* 25504379 [M::ha_hist_line] 72: ********************* 21834552 [M::ha_hist_line] 73: ****************** 18548342 [M::ha_hist_line] 74: *************** 15634383 [M::ha_hist_line] 75: ************* 13085995 [M::ha_hist_line] 76: *********** 10859785 [M::ha_hist_line] 77: ********* 9038664 [M::ha_hist_line] 78: ******* 7500161 [M::ha_hist_line] 79: ****** 6183176 [M::ha_hist_line] 80: ***** 5094558 [M::ha_hist_line] 81: **** 4206133 [M::ha_hist_line] 82: *** 3491588 [M::ha_hist_line] 83: *** 2918827 [M::ha_hist_line] 84: ** 2479447 [M::ha_hist_line] 85: ** 2148066 [M::ha_hist_line] 86: ** 1909666 [M::ha_hist_line] 87: ** 1716070 [M::ha_hist_line] 88: ** 1560886 [M::ha_hist_line] 89: * 1447660 [M::ha_hist_line] 90: * 1370012 [M::ha_hist_line] 91: * 1307447 [M::ha_hist_line] 92: * 1256551 [M::ha_hist_line] 93: * 1228073 [M::ha_hist_line] 94: * 1206383 [M::ha_hist_line] 95: * 1195517 [M::ha_hist_line] 96: * 1188849 [M::ha_hist_line] 97: * 1176168 [M::ha_hist_line] 98: * 1180275 [M::ha_hist_line] 99: * 1170591 [M::ha_hist_line] 100: * 1171299 [M::ha_hist_line] 101: * 1162460 [M::ha_hist_line] 102: * 1157111 [M::ha_hist_line] 103: * 1148604 [M::ha_hist_line] 104: * 1147641 [M::ha_hist_line] 105: * 1136371 [M::ha_hist_line] 106: * 1130620 [M::ha_hist_line] 107: * 1118941 [M::ha_hist_line] 108: * 1108293 [M::ha_hist_line] 109: * 1096344 [M::ha_hist_line] 110: * 1080049 [M::ha_hist_line] 111: * 1058142 [M::ha_hist_line] 112: * 1041859 [M::ha_hist_line] 113: * 1021712 [M::ha_hist_line] 114: * 999093 [M::ha_hist_line] 115: * 978250 [M::ha_hist_line] 116: * 960793 [M::ha_hist_line] 117: * 933716 [M::ha_hist_line] 118: * 912473 [M::ha_hist_line] 119: * 883700 [M::ha_hist_line] 120: * 863615 [M::ha_hist_line] 121: * 832765 [M::ha_hist_line] 122: * 811408 [M::ha_hist_line] 123: * 782470 [M::ha_hist_line] 124: * 756879 [M::ha_hist_line] 125: * 725588 [M::ha_hist_line] 126: * 697855 [M::ha_hist_line] 127: * 669519 [M::ha_hist_line] 128: * 644697 [M::ha_hist_line] 129: * 613066 [M::ha_hist_line] 130: * 591978 [M::ha_hist_line] 131: * 564120 [M::ha_hist_line] 132: * 537024 [M::ha_hist_line] rest: ********************************* 33637165 [M::ha_analyze_count] left: count[10] = 48104334 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 29; peak_het: 10 [M::ha_ct_shrink::4992.35518.34] ==> counted 4792973 distinct minimizer k-mers [M::ha_ft_gen::5002.093[email protected]] ==> filtered out 4792973 k-mers occurring 522 or more times [M::ha_opt_update_cov] updated max_n_chain to 522 [M::yak_count] collected 443389670 minimizers [M::yak_count] collected 144358994 minimizers [M::yak_count] collected 224349201 minimizers [M::yak_count] collected 315355178 minimizers [M::yak_count] collected 402720557 minimizers [M::yak_count] collected 426098822 minimizers [M::yak_count] collected 1161866919 minimizers [M::yak_count] collected 221558942 minimizers [M::yak_count] collected 121455413 minimizers [M::yak_count] collected 209312609 minimizers [M::yak_count] collected 264201380 minimizers [M::yak_count] collected 746200935 minimizers [M::yak_count] collected 490776893 minimizers [M::yak_count] collected 983567481 minimizers [M::yak_count] collected 114927606 minimizers [M::yak_count] collected 126887737 minimizers [M::yak_count] collected 332816365 minimizers [M::yak_count] collected 140315882 minimizers [M::yak_count] collected 745016406 minimizers [M::yak_count] collected 323568444 minimizers [M::ha_pt_gen::6907.84017.10] ==> counted 390120364 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 2088572 [M::ha_analyze_count] highest: count[52] = 4080970

[chhylp123]

I have no idea, either...

[EinarBaldvin]

Hi,

if there are 3 peaks in the kmer spectra it could be that the genome is tetraploid and not diploid, or some degree of genome/chromosomal duplication. You could try and use tools like KAT or findGSE to get some further stats on the genome from the HiFi data.