genome assembled much smaller than expected

[zhaotao1987]

Hello, the genome size of our species estimated by kmer is around 1Gb. Estimated by FCM was 900M. However, using hifiasm we got p_ctg 622M, a_ctg 430M(without HiC), and Hap1 598M and Hap2 587M (with HiC). peak_hom seems okay to me. What might be the reason, over-collapsed the homogenous region? Looking forward to your comments. Thanks!

[M::ha_analyze_count] lowest: count[5] = 1053382 [M::ha_analyze_count] highest: count[24] = 11736026 [M::ha_hist_line] 2: ************************************************************************************** 10050803 [M::ha_hist_line] 3: ****************** 2077604 [M::ha_hist_line] 4: ********** 1213906 [M::ha_hist_line] 5: ********* 1053382 [M::ha_hist_line] 6: ********** 1125957 [M::ha_hist_line] 7: *********** 1247099 [M::ha_hist_line] 8: ************ 1373753 [M::ha_hist_line] 9: ************* 1580790 [M::ha_hist_line] 10: ***************** 1971886 [M::ha_hist_line] 11: ******************** 2362617 [M::ha_hist_line] 12: ************************ 2824735 [M::ha_hist_line] 13: ***************************** 3351481 [M::ha_hist_line] 14: ********************************** 4033277 [M::ha_hist_line] 15: ***************************************** 4839261 [M::ha_hist_line] 16: ************************************************ 5683278 [M::ha_hist_line] 17: ********************************************************* 6713715 [M::ha_hist_line] 18: ***************************************************************** 7632907 [M::ha_hist_line] 19: ************************************************************************** 8659963 [M::ha_hist_line] 20: ********************************************************************************** 9575751 [M::ha_hist_line] 21: **************************************************************************************** 10371164 [M::ha_hist_line] 22: ********************************************************************************************** 11072344 [M::ha_hist_line] 23: *************************************************************************************************** 11577426 [M::ha_hist_line] 24: **************************************************************************************************** 11736026 [M::ha_hist_line] 25: **************************************************************************************************** 11719846 [M::ha_hist_line] 26: ************************************************************************************************** 11526111 [M::ha_hist_line] 27: *********************************************************************************************** 11184638 [M::ha_hist_line] 28: ****************************************************************************************** 10556671 [M::ha_hist_line] 29: ************************************************************************************* 9961869 [M::ha_hist_line] 30: ******************************************************************************** 9376227 [M::ha_hist_line] 31: *************************************************************************** 8758919 [M::ha_hist_line] 32: ********************************************************************** 8161995 [M::ha_hist_line] 33: ***************************************************************** 7642387 [M::ha_hist_line] 34: ************************************************************* 7176593 [M::ha_hist_line] 35: ********************************************************** 6783190 [M::ha_hist_line] 36: ******************************************************** 6617540 [M::ha_hist_line] 37: ******************************************************** 6551060 [M::ha_hist_line] 38: ******************************************************** 6542856 [M::ha_hist_line] 39: ******************************************************** 6613216 [M::ha_hist_line] 40: ********************************************************** 6813222 [M::ha_hist_line] 41: ************************************************************ 7032321 [M::ha_hist_line] 42: ************************************************************** 7270051 [M::ha_hist_line] 43: **************************************************************** 7538157 [M::ha_hist_line] 44: ******************************************************************* 7811810 [M::ha_hist_line] 45: ********************************************************************* 8077498 [M::ha_hist_line] 46: *********************************************************************** 8344303 [M::ha_hist_line] 47: ************************************************************************* 8539963 [M::ha_hist_line] 48: ************************************************************************** 8652787 [M::ha_hist_line] 49: ************************************************************************** 8679010 [M::ha_hist_line] 50: ************************************************************************** 8641874 [M::ha_hist_line] 51: ************************************************************************* 8587206 [M::ha_hist_line] 52: ************************************************************************ 8467109 [M::ha_hist_line] 53: ********************************************************************** 8254506 [M::ha_hist_line] 54: ******************************************************************** 8001324 [M::ha_hist_line] 55: ***************************************************************** 7647500 [M::ha_hist_line] 56: ************************************************************** 7264080 [M::ha_hist_line] 57: ********************************************************** 6843423 [M::ha_hist_line] 58: ******************************************************* 6405726 [M::ha_hist_line] 59: *************************************************** 5992530 [M::ha_hist_line] 60: *********************************************** 5550121 [M::ha_hist_line] 61: ******************************************* 5071325 [M::ha_hist_line] 62: *************************************** 4586939 [M::ha_hist_line] 63: *********************************** 4106756 [M::ha_hist_line] 64: ******************************* 3653968 [M::ha_hist_line] 65: **************************** 3271376 [M::ha_hist_line] 66: ************************* 2886905 [M::ha_hist_line] 67: ********************** 2528487 [M::ha_hist_line] 68: ******************* 2207569 [M::ha_hist_line] 69: **************** 1895812 [M::ha_hist_line] 70: ************** 1614679 [M::ha_hist_line] 71: ************ 1369552 [M::ha_hist_line] 72: ********** 1169645 [M::ha_hist_line] 73: ******** 985313 [M::ha_hist_line] 74: ******* 828485 [M::ha_hist_line] 75: ****** 701482 [M::ha_hist_line] 76: ***** 586948 [M::ha_hist_line] 77: **** 501656 [M::ha_hist_line] 78: **** 428898 [M::ha_hist_line] 79: *** 375480 [M::ha_hist_line] 80: *** 325860 [M::ha_hist_line] 81: ** 285947 [M::ha_hist_line] 82: ** 258076 [M::ha_hist_line] 83: ** 226667 [M::ha_hist_line] 84: ** 199431 [M::ha_hist_line] 85: ** 179731 [M::ha_hist_line] 86: * 159223 [M::ha_hist_line] 87: * 146512 [M::ha_hist_line] 88: * 138968 [M::ha_hist_line] 89: * 130167 [M::ha_hist_line] 90: * 122815 [M::ha_hist_line] 91: * 114513 [M::ha_hist_line] 92: * 109808 [M::ha_hist_line] 93: * 103736 [M::ha_hist_line] 94: * 102419 [M::ha_hist_line] 95: * 98978 [M::ha_hist_line] 96: * 97129 [M::ha_hist_line] 97: * 96088 [M::ha_hist_line] 98: * 95029 [M::ha_hist_line] 99: * 93642 [M::ha_hist_line] 100: * 91785 [M::ha_hist_line] 101: * 89700 [M::ha_hist_line] 102: * 88215 [M::ha_hist_line] 103: * 85416 [M::ha_hist_line] 104: * 83447 [M::ha_hist_line] 105: * 81021 [M::ha_hist_line] 106: * 77092 [M::ha_hist_line] 107: * 76336 [M::ha_hist_line] 108: * 74120 [M::ha_hist_line] 109: * 73296 [M::ha_hist_line] 110: * 69447 [M::ha_hist_line] 111: * 66357 [M::ha_hist_line] 112: * 65183 [M::ha_hist_line] 113: * 62491 [M::ha_hist_line] 114: * 60893 [M::ha_hist_line] rest: ****************************** 3528332 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[49] = 8679010 [M::ha_ft_gen] peak_hom: 49; peak_het: 24 [M::ha_ft_gen::1395.647[email protected]] ==> filtered out 1362229 k-mers occurring 245 or more times [M::ha_opt_update_cov] updated max_n_chain to 245 [M::ha_pt_gen::1960.1648.24] ==> counted 43066104 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 74063 [M::ha_analyze_count] highest: count[24] = 512302 [M::ha_hist_line] 1: ****************************************************************************************************> 23329651 [M::ha_hist_line] 2: *************************************************************************************************> 936808 [M::ha_hist_line] 3: ******************************************* 221448 [M::ha_hist_line] 4: ********************* 106418 [M::ha_hist_line] 5: *************** 77970 [M::ha_hist_line] 6: ************** 74063 [M::ha_hist_line] 7: *************** 76240 [M::ha_hist_line] 8: **************** 79656 [M::ha_hist_line] 9: ***************** 87593 [M::ha_hist_line] 10: ******************** 104971 [M::ha_hist_line] 11: ************************ 121557 [M::ha_hist_line] 12: **************************** 141337 [M::ha_hist_line] 13: ******************************** 163705 [M::ha_hist_line] 14: ************************************** 193108 [M::ha_hist_line] 15: ******************************************** 226931 [M::ha_hist_line] 16: **************************************************** 263979 [M::ha_hist_line] 17: ************************************************************ 308235 [M::ha_hist_line] 18: ******************************************************************** 347919 [M::ha_hist_line] 19: **************************************************************************** 389871 [M::ha_hist_line] 20: ************************************************************************************ 428678 [M::ha_hist_line] 21: ****************************************************************************************** 461265 [M::ha_hist_line] 22: *********************************************************************************************** 488716 [M::ha_hist_line] 23: *************************************************************************************************** 506821 [M::ha_hist_line] 24: **************************************************************************************************** 512302 [M::ha_hist_line] 25: *************************************************************************************************** 509217 [M::ha_hist_line] 26: ************************************************************************************************* 498035 [M::ha_hist_line] 27: ********************************************************************************************** 479291 [M::ha_hist_line] 28: **************************************************************************************** 450703 [M::ha_hist_line] 29: *********************************************************************************** 423246 [M::ha_hist_line] 30: ***************************************************************************** 394812 [M::ha_hist_line] 31: ************************************************************************ 367729 [M::ha_hist_line] 32: ******************************************************************* 340915 [M::ha_hist_line] 33: ************************************************************** 316879 [M::ha_hist_line] 34: ********************************************************** 296142 [M::ha_hist_line] 35: ******************************************************* 279217 [M::ha_hist_line] 36: ***************************************************** 270937 [M::ha_hist_line] 37: **************************************************** 266149 [M::ha_hist_line] 38: **************************************************** 265296 [M::ha_hist_line] 39: **************************************************** 268288 [M::ha_hist_line] 40: ****************************************************** 274244 [M::ha_hist_line] 41: ******************************************************* 282470 [M::ha_hist_line] 42: ********************************************************* 291537 [M::ha_hist_line] 43: *********************************************************** 299840 [M::ha_hist_line] 44: ************************************************************* 310957 [M::ha_hist_line] 45: *************************************************************** 320626 [M::ha_hist_line] 46: **************************************************************** 329564 [M::ha_hist_line] 47: ****************************************************************** 336225 [M::ha_hist_line] 48: ****************************************************************** 338630 [M::ha_hist_line] 49: ****************************************************************** 337927 [M::ha_hist_line] 50: ****************************************************************** 336151 [M::ha_hist_line] 51: ***************************************************************** 333007 [M::ha_hist_line] 52: **************************************************************** 326865 [M::ha_hist_line] 53: ************************************************************** 316859 [M::ha_hist_line] 54: ************************************************************ 307118 [M::ha_hist_line] 55: ********************************************************* 292865 [M::ha_hist_line] 56: ****************************************************** 276732 [M::ha_hist_line] 57: *************************************************** 259905 [M::ha_hist_line] 58: *********************************************** 243244 [M::ha_hist_line] 59: ******************************************** 226868 [M::ha_hist_line] 60: ***************************************** 208737 [M::ha_hist_line] 61: ************************************* 191122 [M::ha_hist_line] 62: ********************************* 171481 [M::ha_hist_line] 63: ****************************** 153480 [M::ha_hist_line] 64: *************************** 136509 [M::ha_hist_line] 65: ************************ 121631 [M::ha_hist_line] 66: ********************* 107088 [M::ha_hist_line] 67: ****************** 94077 [M::ha_hist_line] 68: **************** 81753 [M::ha_hist_line] 69: ************** 70678 [M::ha_hist_line] 70: ************ 59963 [M::ha_hist_line] 71: ********** 51015 [M::ha_hist_line] 72: ********* 43662 [M::ha_hist_line] 73: ******* 36564 [M::ha_hist_line] 74: ****** 31385 [M::ha_hist_line] 75: ***** 26526 [M::ha_hist_line] 76: **** 22311 [M::ha_hist_line] 77: **** 19465 [M::ha_hist_line] 78: *** 16855 [M::ha_hist_line] 79: *** 15002 [M::ha_hist_line] 80: *** 13118 [M::ha_hist_line] 81: ** 11672 [M::ha_hist_line] 82: ** 10603 [M::ha_hist_line] 83: ** 9433 [M::ha_hist_line] 84: ** 8323 [M::ha_hist_line] 85: ** 7833 [M::ha_hist_line] 86: * 6944 [M::ha_hist_line] 87: * 6588 [M::ha_hist_line] 88: * 6128 [M::ha_hist_line] 89: * 5762 [M::ha_hist_line] 90: * 5538 [M::ha_hist_line] 91: * 5279 [M::ha_hist_line] 92: * 5029 [M::ha_hist_line] 93: * 4852 [M::ha_hist_line] 94: * 4587 [M::ha_hist_line] 95: * 4537 [M::ha_hist_line] 96: * 4604 [M::ha_hist_line] 97: * 4307 [M::ha_hist_line] 98: * 4346 [M::ha_hist_line] 99: * 4156 [M::ha_hist_line] 100: * 4185 [M::ha_hist_line] 101: * 4057 [M::ha_hist_line] 102: * 4048 [M::ha_hist_line] 103: * 3873 [M::ha_hist_line] 104: * 3721 [M::ha_hist_line] 105: * 3745 [M::ha_hist_line] 106: * 3502 [M::ha_hist_line] 107: * 3411 [M::ha_hist_line] 108: * 3294 [M::ha_hist_line] 109: * 3238 [M::ha_hist_line] 110: * 3031 [M::ha_hist_line] 111: * 3006 [M::ha_hist_line] 112: * 2973 [M::ha_hist_line] 113: * 2921 [M::ha_hist_line] 114: * 2827 [M::ha_hist_line] 115: * 2630 [M::ha_hist_line] 116: * 2591 [M::ha_hist_line] rest: ******************* 98376 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[48] = 338630 [M::ha_pt_gen] peak_hom: 48; peak_het: 24 [M::ha_pt_gen::2119.3239.46] ==> indexed 701600102 positions [M::ha_assemble::10698.161[email protected]] ==> corrected reads for round 1 [M::ha_assemble] # bases: 28074457717; # corrected bases: 92313868; # recorrected bases: 88171 [M::ha_assemble] size of buffer: 23.924GB [M::ha_pt_gen::10822.60233.84] ==> counted 21698053 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 46653 [M::ha_analyze_count] highest: count[25] = 500859 [M::ha_hist_line] 1: *************************************************************************************************> 3086305 [M::ha_hist_line] 2: *************************** 137092 [M::ha_hist_line] 3: *********** 53973 [M::ha_hist_line] 4: ********* 45352 [M::ha_hist_line] 5: ********* 46653 [M::ha_hist_line] 6: *********** 53619 [M::ha_hist_line] 7: ************ 62185 [M::ha_hist_line] 8: ************* 67343 [M::ha_hist_line] 9: *************** 73864 [M::ha_hist_line] 10: ****************** 91729 [M::ha_hist_line] 11: ********************** 108041 [M::ha_hist_line] 12: ************************* 124962 [M::ha_hist_line] 13: ***************************** 143636 [M::ha_hist_line] 14: ********************************** 170239 [M::ha_hist_line] 15: **************************************** 201288 [M::ha_hist_line] 16: ********************************************** 230712 [M::ha_hist_line] 17: ******************************************************* 276457 [M::ha_hist_line] 18: ************************************************************** 312339 [M::ha_hist_line] 19: ********************************************************************** 353091 [M::ha_hist_line] 20: ******************************************************************************* 395553 [M::ha_hist_line] 21: ************************************************************************************* 427259 [M::ha_hist_line] 22: ******************************************************************************************* 456036 [M::ha_hist_line] 23: ************************************************************************************************* 486370 [M::ha_hist_line] 24: *************************************************************************************************** 498334 [M::ha_hist_line] 25: **************************************************************************************************** 500859 [M::ha_hist_line] 26: *************************************************************************************************** 494524 [M::ha_hist_line] 27: ************************************************************************************************* 486626 [M::ha_hist_line] 28: ********************************************************************************************* 463440 [M::ha_hist_line] 29: *************************************************************************************** 433997 [M::ha_hist_line] 30: ********************************************************************************** 410819 [M::ha_hist_line] 31: **************************************************************************** 380717 [M::ha_hist_line] 32: *********************************************************************** 355592 [M::ha_hist_line] 33: ****************************************************************** 331091 [M::ha_hist_line] 34: ************************************************************* 307922 [M::ha_hist_line] 35: ********************************************************* 284217 [M::ha_hist_line] 36: ****************************************************** 270764 [M::ha_hist_line] 37: ***************************************************** 263352 [M::ha_hist_line] 38: *************************************************** 256839 [M::ha_hist_line] 39: *************************************************** 254961 [M::ha_hist_line] 40: **************************************************** 258191 [M::ha_hist_line] 41: ***************************************************** 263645 [M::ha_hist_line] 42: ****************************************************** 271132 [M::ha_hist_line] 43: ******************************************************** 282008 [M::ha_hist_line] 44: ********************************************************* 287995 [M::ha_hist_line] 45: *********************************************************** 297971 [M::ha_hist_line] 46: ************************************************************** 311872 [M::ha_hist_line] 47: **************************************************************** 318823 [M::ha_hist_line] 48: ***************************************************************** 327108 [M::ha_hist_line] 49: ****************************************************************** 331542 [M::ha_hist_line] 50: ****************************************************************** 330970 [M::ha_hist_line] 51: ****************************************************************** 329967 [M::ha_hist_line] 52: ****************************************************************** 329782 [M::ha_hist_line] 53: ***************************************************************** 324552 [M::ha_hist_line] 54: *************************************************************** 317589 [M::ha_hist_line] 55: ************************************************************** 308314 [M::ha_hist_line] 56: *********************************************************** 294427 [M::ha_hist_line] 57: ******************************************************** 279260 [M::ha_hist_line] 58: ***************************************************** 264769 [M::ha_hist_line] 59: ************************************************** 248624 [M::ha_hist_line] 60: ********************************************** 232498 [M::ha_hist_line] 61: ******************************************* 216786 [M::ha_hist_line] 62: **************************************** 198965 [M::ha_hist_line] 63: ************************************ 181926 [M::ha_hist_line] 64: ******************************** 162732 [M::ha_hist_line] 65: ***************************** 146101 [M::ha_hist_line] 66: ************************** 130226 [M::ha_hist_line] 67: *********************** 117449 [M::ha_hist_line] 68: ******************** 102083 [M::ha_hist_line] 69: ****************** 88822 [M::ha_hist_line] 70: *************** 77598 [M::ha_hist_line] 71: ************* 67175 [M::ha_hist_line] 72: *********** 57445 [M::ha_hist_line] 73: ********** 47819 [M::ha_hist_line] 74: ******** 42016 [M::ha_hist_line] 75: ******* 35523 [M::ha_hist_line] 76: ****** 29891 [M::ha_hist_line] 77: ***** 25323 [M::ha_hist_line] 78: **** 21841 [M::ha_hist_line] 79: **** 18356 [M::ha_hist_line] 80: *** 16251 [M::ha_hist_line] 81: *** 14384 [M::ha_hist_line] 82: *** 12700 [M::ha_hist_line] 83: ** 11570 [M::ha_hist_line] 84: ** 10512 [M::ha_hist_line] 85: ** 9305 [M::ha_hist_line] 86: ** 8132 [M::ha_hist_line] 87: * 7458 [M::ha_hist_line] 88: * 6738 [M::ha_hist_line] 89: * 6375 [M::ha_hist_line] 90: * 6238 [M::ha_hist_line] 91: * 5869 [M::ha_hist_line] 92: * 5475 [M::ha_hist_line] 93: * 5220 [M::ha_hist_line] 94: * 4975 [M::ha_hist_line] 95: * 4589 [M::ha_hist_line] 96: * 4649 [M::ha_hist_line] 97: * 4273 [M::ha_hist_line] 98: * 4343 [M::ha_hist_line] 99: * 4455 [M::ha_hist_line] 100: * 4438 [M::ha_hist_line] 101: * 4224 [M::ha_hist_line] 102: * 4140 [M::ha_hist_line] 103: * 3925 [M::ha_hist_line] 104: * 4070 [M::ha_hist_line] 105: * 3809 [M::ha_hist_line] 106: * 3804 [M::ha_hist_line] 107: * 3527 [M::ha_hist_line] 108: * 3465 [M::ha_hist_line] 109: * 3379 [M::ha_hist_line] 110: * 3507 [M::ha_hist_line] 111: * 3214 [M::ha_hist_line] 112: * 3018 [M::ha_hist_line] 113: * 3004 [M::ha_hist_line] 114: * 2976 [M::ha_hist_line] 115: * 3059 [M::ha_hist_line] 116: * 2823 [M::ha_hist_line] 117: * 2721 [M::ha_hist_line] 118: * 2537 [M::ha_hist_line] rest: ******************** 101634 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[49] = 331542 [M::ha_pt_gen] peak_hom: 49; peak_het: 25 [M::ha_pt_gen::10972.43233.72] ==> indexed 718857534 positions [M::ha_assemble::18146.739[email protected]] ==> corrected reads for round 2 [M::ha_assemble] # bases: 28043627507; # corrected bases: 4532773; # recorrected bases: 6883 [M::ha_assemble] size of buffer: 24.340GB [M::ha_pt_gen::18259.96336.13] ==> counted 20457954 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 42457 [M::ha_analyze_count] highest: count[25] = 500521 [M::ha_hist_line] 1: *************************************************************************************************> 1920579 [M::ha_hist_line] 2: ******************** 101153 [M::ha_hist_line] 3: ******** 40955 [M::ha_hist_line] 4: ******** 38254 [M::ha_hist_line] 5: ******** 42457 [M::ha_hist_line] 6: ********** 50624 [M::ha_hist_line] 7: ************ 59968 [M::ha_hist_line] 8: ************* 65273 [M::ha_hist_line] 9: ************** 72288 [M::ha_hist_line] 10: ****************** 90565 [M::ha_hist_line] 11: ********************* 106914 [M::ha_hist_line] 12: ************************* 124012 [M::ha_hist_line] 13: **************************** 142330 [M::ha_hist_line] 14: ********************************** 169329 [M::ha_hist_line] 15: **************************************** 200034 [M::ha_hist_line] 16: ********************************************** 229055 [M::ha_hist_line] 17: ******************************************************* 275076 [M::ha_hist_line] 18: ************************************************************** 310998 [M::ha_hist_line] 19: ********************************************************************** 351377 [M::ha_hist_line] 20: ******************************************************************************* 393524 [M::ha_hist_line] 21: ************************************************************************************* 425234 [M::ha_hist_line] 22: ******************************************************************************************* 454952 [M::ha_hist_line] 23: ************************************************************************************************* 485200 [M::ha_hist_line] 24: *************************************************************************************************** 497269 [M::ha_hist_line] 25: **************************************************************************************************** 500521 [M::ha_hist_line] 26: *************************************************************************************************** 494112 [M::ha_hist_line] 27: ************************************************************************************************* 486345 [M::ha_hist_line] 28: ********************************************************************************************* 463648 [M::ha_hist_line] 29: *************************************************************************************** 434425 [M::ha_hist_line] 30: ********************************************************************************** 410643 [M::ha_hist_line] 31: **************************************************************************** 382279 [M::ha_hist_line] 32: *********************************************************************** 355498 [M::ha_hist_line] 33: ****************************************************************** 331619 [M::ha_hist_line] 34: ************************************************************** 308915 [M::ha_hist_line] 35: ********************************************************* 284100 [M::ha_hist_line] 36: ****************************************************** 270775 [M::ha_hist_line] 37: ***************************************************** 262989 [M::ha_hist_line] 38: *************************************************** 256572 [M::ha_hist_line] 39: *************************************************** 254544 [M::ha_hist_line] 40: *************************************************** 257203 [M::ha_hist_line] 41: ***************************************************** 262811 [M::ha_hist_line] 42: ****************************************************** 270439 [M::ha_hist_line] 43: ******************************************************** 280802 [M::ha_hist_line] 44: ********************************************************* 286643 [M::ha_hist_line] 45: *********************************************************** 296932 [M::ha_hist_line] 46: ************************************************************** 310787 [M::ha_hist_line] 47: *************************************************************** 317800 [M::ha_hist_line] 48: ***************************************************************** 325879 [M::ha_hist_line] 49: ****************************************************************** 330787 [M::ha_hist_line] 50: ****************************************************************** 330426 [M::ha_hist_line] 51: ****************************************************************** 330711 [M::ha_hist_line] 52: ****************************************************************** 329615 [M::ha_hist_line] 53: ***************************************************************** 324516 [M::ha_hist_line] 54: *************************************************************** 317668 [M::ha_hist_line] 55: ************************************************************** 309051 [M::ha_hist_line] 56: *********************************************************** 294658 [M::ha_hist_line] 57: ******************************************************** 279653 [M::ha_hist_line] 58: ***************************************************** 265941 [M::ha_hist_line] 59: ************************************************** 249201 [M::ha_hist_line] 60: *********************************************** 233618 [M::ha_hist_line] 61: ******************************************** 217894 [M::ha_hist_line] 62: **************************************** 200615 [M::ha_hist_line] 63: ************************************* 183093 [M::ha_hist_line] 64: ********************************* 164193 [M::ha_hist_line] 65: ***************************** 147431 [M::ha_hist_line] 66: ************************** 130930 [M::ha_hist_line] 67: ************************ 118825 [M::ha_hist_line] 68: ********************* 103713 [M::ha_hist_line] 69: ****************** 89935 [M::ha_hist_line] 70: **************** 78545 [M::ha_hist_line] 71: ************** 68072 [M::ha_hist_line] 72: ************ 58172 [M::ha_hist_line] 73: ********** 49043 [M::ha_hist_line] 74: ********* 42765 [M::ha_hist_line] 75: ******* 35920 [M::ha_hist_line] 76: ****** 30307 [M::ha_hist_line] 77: ***** 25700 [M::ha_hist_line] 78: **** 22107 [M::ha_hist_line] 79: **** 18710 [M::ha_hist_line] 80: *** 16419 [M::ha_hist_line] 81: *** 14537 [M::ha_hist_line] 82: *** 12816 [M::ha_hist_line] 83: ** 11593 [M::ha_hist_line] 84: ** 10723 [M::ha_hist_line] 85: ** 9312 [M::ha_hist_line] 86: ** 8320 [M::ha_hist_line] 87: * 7501 [M::ha_hist_line] 88: * 6755 [M::ha_hist_line] 89: * 6427 [M::ha_hist_line] 90: * 6173 [M::ha_hist_line] 91: * 5971 [M::ha_hist_line] 92: * 5480 [M::ha_hist_line] 93: * 5290 [M::ha_hist_line] 94: * 4938 [M::ha_hist_line] 95: * 4657 [M::ha_hist_line] 96: * 4602 [M::ha_hist_line] 97: * 4328 [M::ha_hist_line] 98: * 4294 [M::ha_hist_line] 99: * 4382 [M::ha_hist_line] 100: * 4458 [M::ha_hist_line] 101: * 4169 [M::ha_hist_line] 102: * 4214 [M::ha_hist_line] 103: * 3947 [M::ha_hist_line] 104: * 4083 [M::ha_hist_line] 105: * 3866 [M::ha_hist_line] 106: * 3763 [M::ha_hist_line] 107: * 3565 [M::ha_hist_line] 108: * 3442 [M::ha_hist_line] 109: * 3371 [M::ha_hist_line] 110: * 3551 [M::ha_hist_line] 111: * 3265 [M::ha_hist_line] 112: * 3006 [M::ha_hist_line] 113: * 3014 [M::ha_hist_line] 114: * 2935 [M::ha_hist_line] 115: * 3073 [M::ha_hist_line] 116: * 2807 [M::ha_hist_line] 117: * 2729 [M::ha_hist_line] 118: * 2568 [M::ha_hist_line] rest: ******************** 102094 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[49] = 330787 [M::ha_pt_gen] peak_hom: 49; peak_het: 25 [M::ha_pt_gen::18386.72836.08] ==> indexed 719517199 positions [M::ha_assemble::26348.950[email protected]] ==> corrected reads for round 3 [M::ha_assemble] # bases: 28041832923; # corrected bases: 286504; # recorrected bases: 8334 [M::ha_assemble] size of buffer: 24.243GB [M::ha_pt_gen::26459.27637.22] ==> counted 20372651 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[5] = 40865 [M::ha_analyze_count] highest: count[25] = 500501 [M::ha_hist_line] 1: **************************************************************************************************> 1858325 [M::ha_hist_line] 2: ****************** 91092 [M::ha_hist_line] 3: ******* 36253 [M::ha_hist_line] 4: ******* 36115 [M::ha_hist_line] 5: ******** 40865 [M::ha_hist_line] 6: ********** 49518 [M::ha_hist_line] 7: ************ 59161 [M::ha_hist_line] 8: ************* 64968 [M::ha_hist_line] 9: ************** 71860 [M::ha_hist_line] 10: ****************** 90358 [M::ha_hist_line] 11: ********************* 106593 [M::ha_hist_line] 12: ************************* 123770 [M::ha_hist_line] 13: **************************** 142102 [M::ha_hist_line] 14: ********************************** 169285 [M::ha_hist_line] 15: **************************************** 199918 [M::ha_hist_line] 16: ********************************************** 228924 [M::ha_hist_line] 17: ******************************************************* 274990 [M::ha_hist_line] 18: ************************************************************** 311024 [M::ha_hist_line] 19: ********************************************************************** 351136 [M::ha_hist_line] 20: ******************************************************************************* 393476 [M::ha_hist_line] 21: ************************************************************************************* 425112 [M::ha_hist_line] 22: ******************************************************************************************* 454970 [M::ha_hist_line] 23: ************************************************************************************************* 485095 [M::ha_hist_line] 24: *************************************************************************************************** 497141 [M::ha_hist_line] 25: **************************************************************************************************** 500501 [M::ha_hist_line] 26: *************************************************************************************************** 494021 [M::ha_hist_line] 27: ************************************************************************************************* 486264 [M::ha_hist_line] 28: ********************************************************************************************* 463585 [M::ha_hist_line] 29: *************************************************************************************** 434357 [M::ha_hist_line] 30: ********************************************************************************** 410568 [M::ha_hist_line] 31: **************************************************************************** 382423 [M::ha_hist_line] 32: *********************************************************************** 355521 [M::ha_hist_line] 33: ****************************************************************** 331668 [M::ha_hist_line] 34: ************************************************************** 308890 [M::ha_hist_line] 35: ********************************************************* 284095 [M::ha_hist_line] 36: ****************************************************** 270775 [M::ha_hist_line] 37: ***************************************************** 262922 [M::ha_hist_line] 38: *************************************************** 256596 [M::ha_hist_line] 39: *************************************************** 254507 [M::ha_hist_line] 40: *************************************************** 257183 [M::ha_hist_line] 41: ***************************************************** 262835 [M::ha_hist_line] 42: ****************************************************** 270507 [M::ha_hist_line] 43: ******************************************************** 280694 [M::ha_hist_line] 44: ********************************************************* 286696 [M::ha_hist_line] 45: *********************************************************** 296868 [M::ha_hist_line] 46: ************************************************************** 310832 [M::ha_hist_line] 47: *************************************************************** 317773 [M::ha_hist_line] 48: ***************************************************************** 325809 [M::ha_hist_line] 49: ****************************************************************** 330785 [M::ha_hist_line] 50: ****************************************************************** 330476 [M::ha_hist_line] 51: ****************************************************************** 330694 [M::ha_hist_line] 52: ****************************************************************** 329615 [M::ha_hist_line] 53: ***************************************************************** 324493 [M::ha_hist_line] 54: *************************************************************** 317697 [M::ha_hist_line] 55: ************************************************************** 309073 [M::ha_hist_line] 56: *********************************************************** 294650 [M::ha_hist_line] 57: ******************************************************** 279676 [M::ha_hist_line] 58: ***************************************************** 265904 [M::ha_hist_line] 59: ************************************************** 249232 [M::ha_hist_line] 60: *********************************************** 233722 [M::ha_hist_line] 61: ******************************************** 217850 [M::ha_hist_line] 62: **************************************** 200614 [M::ha_hist_line] 63: ************************************* 183174 [M::ha_hist_line] 64: ********************************* 164210 [M::ha_hist_line] 65: ***************************** 147506 [M::ha_hist_line] 66: ************************** 130886 [M::ha_hist_line] 67: ************************ 118831 [M::ha_hist_line] 68: ********************* 103793 [M::ha_hist_line] 69: ****************** 89952 [M::ha_hist_line] 70: **************** 78561 [M::ha_hist_line] 71: ************** 68050 [M::ha_hist_line] 72: ************ 58184 [M::ha_hist_line] 73: ********** 49071 [M::ha_hist_line] 74: ********* 42771 [M::ha_hist_line] 75: ******* 35908 [M::ha_hist_line] 76: ****** 30326 [M::ha_hist_line] 77: ***** 25692 [M::ha_hist_line] 78: **** 22129 [M::ha_hist_line] 79: **** 18706 [M::ha_hist_line] 80: *** 16429 [M::ha_hist_line] 81: *** 14548 [M::ha_hist_line] 82: *** 12784 [M::ha_hist_line] 83: ** 11616 [M::ha_hist_line] 84: ** 10729 [M::ha_hist_line] 85: ** 9309 [M::ha_hist_line] 86: ** 8321 [M::ha_hist_line] 87: * 7507 [M::ha_hist_line] 88: * 6741 [M::ha_hist_line] 89: * 6417 [M::ha_hist_line] 90: * 6205 [M::ha_hist_line] 91: * 5986 [M::ha_hist_line] 92: * 5467 [M::ha_hist_line] 93: * 5293 [M::ha_hist_line] 94: * 4942 [M::ha_hist_line] 95: * 4647 [M::ha_hist_line] 96: * 4602 [M::ha_hist_line] 97: * 4321 [M::ha_hist_line] 98: * 4286 [M::ha_hist_line] 99: * 4389 [M::ha_hist_line] 100: * 4459 [M::ha_hist_line] 101: * 4169 [M::ha_hist_line] 102: * 4215 [M::ha_hist_line] 103: * 3959 [M::ha_hist_line] 104: * 4088 [M::ha_hist_line] 105: * 3860 [M::ha_hist_line] 106: * 3748 [M::ha_hist_line] 107: * 3565 [M::ha_hist_line] 108: * 3452 [M::ha_hist_line] 109: * 3359 [M::ha_hist_line] 110: * 3552 [M::ha_hist_line] 111: * 3253 [M::ha_hist_line] 112: * 3016 [M::ha_hist_line] 113: * 3006 [M::ha_hist_line] 114: * 2943 [M::ha_hist_line] 115: * 3084 [M::ha_hist_line] 116: * 2799 [M::ha_hist_line] 117: * 2735 [M::ha_hist_line] 118: * 2563 [M::ha_hist_line] rest: ******************** 102115 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[49] = 330785 [M::ha_pt_gen] peak_hom: 49; peak_het: 25 [M::ha_pt_gen::26589.52637.17] ==> indexed 719436566 positions [M::ha_assemble::27532.502[email protected]] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 87382743 [M::ha_print_ovlp_stat] # strong overlaps: 39994884 [M::ha_print_ovlp_stat] # weak overlaps: 47387859 [M::ha_print_ovlp_stat] # exact overlaps: 84015619 [M::ha_print_ovlp_stat] # inexact overlaps: 3367124 [M::ha_print_ovlp_stat] # overlaps without large indels: 87207871 [M::ha_print_ovlp_stat] # reverse overlaps: 28942832 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. Writing raw unitig GFA to disk... Writing processed unitig GFA to disk... [M::purge_dups] purge duplication coverage threshold: 61 [M::adjust_utg_by_primary] primary contig coverage range: [38, infinity] [M::purge_dups] purge duplication coverage threshold: 61 [M::purge_dups] purge duplication coverage threshold: 61 [M::purge_dups] purge duplication coverage threshold: 61 [M::purge_dups] purge duplication coverage threshold: 61 [M::adjust_utg_by_primary] primary contig coverage range: [38, infinity] Writing primary contig GFA to disk... Writing alternate contig GFA to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.14-r312 [M::main] CMD: hifiasm -o /ngsproject/zhaot/assem_annot_pipeline/project/Pseudocydonia_sinensis/output/Psin.asm -t 40 -l 0 /ngsproject/zhaot/genome_projects/Pseudocydonia_sinensis/CCS/BMK_DATA_20211028143407_1/Data/BMK210908-AN714-01P0001-01/cell/BMK210908-AN714-01P0001-01.ccs.fastq.gz [M::main] Real time: 28164.749 sec; CPU: 1026670.822 sec; Peak RSS: 70.023 GB

[chhylp123]

I haven't seen HiFi assemblies with ~40% regions that are collapsed... Probably some other parts are wrong.

[zhaotao1987]

Thanks for the reply! Very glad that the problem was solved! I thought --hom-cov would work and is crucial for the assembling. At first I've used the command like this: I [M::main] CMD: hifiasm -o hifi_new -t 40 -l0 --hg-size 900m --hom-cov 49 data.ccs.fastq but it actually didn't work, until I used -D 10, then I got the correct sized assembly. [M::main] CMD: hifiasm -o hifi_new -t 40 -l0 --hg-size 980m -D 10 data.ccs.fastq I just wondered why it has such a big impact on the assembling in my case.

[chhylp123]

The most important part is how to determine the homozygous coverage. For your case, probably hifiasm could automatically identify the homozygous coverage with -D10.

[zhaotao1987]

Sorry, I was probably wrong. Maybe the genome size was over-estimated, the kmer plot (for genome-size estimation) was made using hifi data, maybe led to a different result compared to illumina data(?). I used -D 10 to get a bigger size genome (880m), but the dotplot looks not very good, compared to the assembly of 620m. I just wondered, (maybe you could help me check the running log above again), from the hifiasm kmer curve, the homozygous peak should be around 50, is that right? Since that kmer curve in hifiasm peaks differently from GenomeScope (25/50 compared to 12.5/25), I'm not sure whether kmer plot using minimizers (as used in hifiasm) may always double the peak values from normal kmer plots? Thanks a lot !

Dotplots comparing the assembly (y) with reference (x axis)