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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Is such a k-mer plot normal? #575

Open YanCheer opened 11 months ago

YanCheer commented 11 months ago

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

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

[M::ha_analyze_count] lowest: count[6] = 2125610 [M::ha_analyze_count] highest: count[47] = 27712519 [M::ha_hist_line] 2: **** 5453856 [M::ha_hist_line] 3: * 2600588 [M::ha_hist_line] 4: **** 2298149 [M::ha_hist_line] 5: **** 2146925 [M::ha_hist_line] 6: **** 2125610 [M::ha_hist_line] 7: **** 2192293 [M::ha_hist_line] 8: * 2424623 [M::ha_hist_line] 9: ** 2702840 [M::ha_hist_line] 10: * 3122281 [M::ha_hist_line] 11: *** 3660448 [M::ha_hist_line] 12: **** 4469464 [M::ha_hist_line] 13: **** 5472872 [M::ha_hist_line] 14: **** 6680176 [M::ha_hist_line] 15: ** 8305315 [M::ha_hist_line] 16: **** 10049299 [M::ha_hist_line] 17: * 11928773 [M::ha_hist_line] 18: ** 13939095 [M::ha_hist_line] 19: *** 15725702 [M::ha_hist_line] 20: * 17448468 [M::ha_hist_line] 21: ***** 18649639 [M::ha_hist_line] 22: ** 19445261 [M::ha_hist_line] 23: **** 19928678 [M::ha_hist_line] 24: ** 19778630 [M::ha_hist_line] 25: 19162189 [M::ha_hist_line] 26: ** 18155434 [M::ha_hist_line] 27: ** 17106676 [M::ha_hist_line] 28: ***** 15787893 [M::ha_hist_line] 29: **** 14536096 [M::ha_hist_line] 30: * 13543114 [M::ha_hist_line] 31: ** 12833846 [M::ha_hist_line] 32: * 12383060 [M::ha_hist_line] 33: **** 12307665 [M::ha_hist_line] 34: ** 12692762 [M::ha_hist_line] 35: **** 13412706 [M::ha_hist_line] 36: **** 14403120 [M::ha_hist_line] 37: ***** 15678271 [M::ha_hist_line] 38: ** 17147659 [M::ha_hist_line] 39: **** 18748237 [M::ha_hist_line] 40: ** 20384351 [M::ha_hist_line] 41: * 21998624 [M::ha_hist_line] 42: *** 23604249 [M::ha_hist_line] 43: ** 25038333 [M::ha_hist_line] 44: * 26265158 [M::ha_hist_line] 45: ** 27027200 [M::ha_hist_line] 46: **** 27581400 [M::ha_hist_line] 47: **** 27712519 [M::ha_hist_line] 48: ***** 27472275 [M::ha_hist_line] 49: ***** 26871390 [M::ha_hist_line] 50: ** 26100679 [M::ha_hist_line] 51: * 24787360 [M::ha_hist_line] 52: *** 23086431 [M::ha_hist_line] 53: * 21261823 [M::ha_hist_line] 54: ** 19414101 [M::ha_hist_line] 55: ***** 17332103 [M::ha_hist_line] 56: * 15303278 [M::ha_hist_line] 57: **** 13391423 [M::ha_hist_line] 58: *** 11495486 [M::ha_hist_line] 59: * 9809959 [M::ha_hist_line] 60: ** 8287287 [M::ha_hist_line] 61: ***** 6913725 [M::ha_hist_line] 62: **** 5677361 [M::ha_hist_line] 63: * 4696075 [M::ha_hist_line] 64: ** 3753339 [M::ha_hist_line] 65: ** 3008953 [M::ha_hist_line] 66: 2371004 [M::ha_hist_line] 67: ** 1866927 [M::ha_hist_line] 68: 1451842 [M::ha_hist_line] 69: 1136616 [M::ha_hist_line] 70: 866428 [M::ha_hist_line] 71: 649436 [M::ha_hist_line] 72: 508225 [M::ha_hist_line] 73: 414301 [M::ha_hist_line] 74: 333182 [M::ha_hist_line] 75: 271241 [M::ha_hist_line] 76: 223738 [M::ha_hist_line] 77: 188763 [M::ha_hist_line] 78: 163899 [M::ha_hist_line] 79: 146305 [M::ha_hist_line] rest: 7012300 [M::ha_analyze_count] left: count[23] = 19928678 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::1626.44813.41] ==> counted 1976416 distinct minimizer k-mers [M::ha_ft_gen::1630.56813.38@32.848GB] ==> filtered out 1976416 k-mers occurring 235 or more times [M::ha_opt_update_cov] updated max_n_chain to 235 [M::yak_count] collected 1463544421 minimizers [M::ha_pt_gen::2235.47113.21] ==> counted 55746676 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 130163 [M::ha_analyze_count] highest: count[47] = 1068344 [M::ha_hist_line] 1: **> 17590237 [M::ha_hist_line] 2: ** 488757 [M::ha_hist_line] 3: * 185485 [M::ha_hist_line] 4: ** 146999 [M::ha_hist_line] 5: * 133769 [M::ha_hist_line] 6: **** 130163 [M::ha_hist_line] 7: **** 132424 [M::ha_hist_line] 8: * 142810 [M::ha_hist_line] 9: *** 155736 [M::ha_hist_line] 10: **** 174729 [M::ha_hist_line] 11: * 198893 [M::ha_hist_line] 12: ** 233747 [M::ha_hist_line] 13: ** 278861 [M::ha_hist_line] 14: ***** 332935 [M::ha_hist_line] 15: ** 402040 [M::ha_hist_line] 16: * 478270 [M::ha_hist_line] 17: **** 557802 [M::ha_hist_line] 18: **** 643177 [M::ha_hist_line] 19: *** 715900 [M::ha_hist_line] 20: ** 786085 [M::ha_hist_line] 21: ** 832833 [M::ha_hist_line] 22: * 861256 [M::ha_hist_line] 23: ** 877606 [M::ha_hist_line] 24: * 865461 [M::ha_hist_line] 25: ** 832760 [M::ha_hist_line] 26: ** 786363 [M::ha_hist_line] 27: *** 734688 [M::ha_hist_line] 28: * 676276 [M::ha_hist_line] 29: ** 619602 [M::ha_hist_line] 30: ** 574259 [M::ha_hist_line] 31: * 540310 [M::ha_hist_line] 32: ** 516735 [M::ha_hist_line] 33: **** 511011 [M::ha_hist_line] 34: * 522482 [M::ha_hist_line] 35: * 546378 [M::ha_hist_line] 36: ** 581509 [M::ha_hist_line] 37: ***** 628364 [M::ha_hist_line] 38: **** 683899 [M::ha_hist_line] 39: ** 745376 [M::ha_hist_line] 40: * 806075 [M::ha_hist_line] 41: *** 865272 [M::ha_hist_line] 42: * 925841 [M::ha_hist_line] 43: **** 977733 [M::ha_hist_line] 44: **** 1021154 [M::ha_hist_line] 45: ** 1047960 [M::ha_hist_line] 46: **** 1066546 [M::ha_hist_line] 47: **** 1068344 [M::ha_hist_line] 48: ***** 1054158 [M::ha_hist_line] 49: **** 1029367 [M::ha_hist_line] 50: *** 994303 [M::ha_hist_line] 51: **** 941602 [M::ha_hist_line] 52: ** 875424 [M::ha_hist_line] 53: * 803692 [M::ha_hist_line] 54: **** 731420 [M::ha_hist_line] 55: *** 652223 [M::ha_hist_line] 56: ** 574588 [M::ha_hist_line] 57: * 503016 [M::ha_hist_line] 58: **** 430163 [M::ha_hist_line] 59: *** 368680 [M::ha_hist_line] 60: * 310516 [M::ha_hist_line] 61: **** 259516 [M::ha_hist_line] 62: **** 214562 [M::ha_hist_line] 63: **** 177251 [M::ha_hist_line] 64: 143042 [M::ha_hist_line] 65: ** 115631 [M::ha_hist_line] 66: 92354 [M::ha_hist_line] 67: * 73796 [M::ha_hist_line] 68: ** 59021 [M::ha_hist_line] 69: *** 47314 [M::ha_hist_line] 70: 37247 [M::ha_hist_line] 71: * 29299 [M::ha_hist_line] 72: 24169 [M::ha_hist_line] 73: 20804 [M::ha_hist_line] 74: * 17786 [M::ha_hist_line] 75: 15243 [M::ha_hist_line] 76: 13384 [M::ha_hist_line] 77: 12028 [M::ha_hist_line] 78: 11226 [M::ha_hist_line] 79: 10377 [M::ha_hist_line] 80: 9690 [M::ha_hist_line] 81: 9144 [M::ha_hist_line] 82: 8672 [M::ha_hist_line] 83: 8376 [M::ha_hist_line] 84: 7984 [M::ha_hist_line] 85: 7873 [M::ha_hist_line] 86: 7545 [M::ha_hist_line] 87: 7739 [M::ha_hist_line] 88: 7420 [M::ha_hist_line] 89: 7320 [M::ha_hist_line] 90: 7195 [M::ha_hist_line] 91: 7103 [M::ha_hist_line] 92: 7207 [M::ha_hist_line] 93: 6946 [M::ha_hist_line] 94: 6865 [M::ha_hist_line] 95: 6731 [M::ha_hist_line] 96: 6475 [M::ha_hist_line] 97: 6318 [M::ha_hist_line] 98: 6249 [M::ha_hist_line] 99: 6315 [M::ha_hist_line] 100: 6173 [M::ha_hist_line] 101: 5782 [M::ha_hist_line] 102: 5714 [M::ha_hist_line] 103: 5727 [M::ha_hist_line] 104: 5428 [M::ha_hist_line] 105: 5442 [M::ha_hist_line] rest: ** 295129 [M::ha_analyze_count] left: count[23] = 877606 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::2235.59113.22] ==> counted 38156439 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1463544421 minimizers [M::ha_pt_gen::2465.69114.68] ==> indexed 1445954184 positions, counted 38156439 distinct minimizer k-mers sh 00.Scripts/02.AlltheCells.hifias[M::ha_assemble::4791.52140.60@41.402GB] ==> corrected reads for round 1 [M::ha_assemble] # bases: 54190381756; # corrected bases: 82102298; # recorrected bases: 85786 [M::ha_assemble] size of buffer: 12.223GB [M::yak_count] collected 1462371695 minimizers [M::ha_pt_gen::4933.97640.45] ==> counted 38571258 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 123680 [M::ha_analyze_count] highest: count[47] = 1062125 [M::ha_hist_line] 1: *** 839947 [M::ha_hist_line] 2: ** 153744 [M::ha_hist_line] 3: **** 130830 [M::ha_hist_line] 4: **** 129587 [M::ha_hist_line] 5: **** 124947 [M::ha_hist_line] 6: **** 123680 [M::ha_hist_line] 7: **** 127440 [M::ha_hist_line] 8: * 137878 [M::ha_hist_line] 9: ** 149773 [M::ha_hist_line] 10: **** 168779 [M::ha_hist_line] 11: ** 189920 [M::ha_hist_line] 12: * 224683 [M::ha_hist_line] 13: ***** 266712 [M::ha_hist_line] 14: ** 316186 [M::ha_hist_line] 15: **** 384657 [M::ha_hist_line] 16: * 455486 [M::ha_hist_line] 17: ** 533795 [M::ha_hist_line] 18: ** 618721 [M::ha_hist_line] 19: *** 692610 [M::ha_hist_line] 20: **** 764093 [M::ha_hist_line] 21: * 812885 [M::ha_hist_line] 22: **** 848002 [M::ha_hist_line] 23: ** 869487 [M::ha_hist_line] 24: ***** 864611 [M::ha_hist_line] 25: **** 836815 [M::ha_hist_line] 26: 793494 [M::ha_hist_line] 27: ** 745041 [M::ha_hist_line] 28: *** 686108 [M::ha_hist_line] 29: * 628782 [M::ha_hist_line] 30: **** 578946 [M::ha_hist_line] 31: 544256 [M::ha_hist_line] 32: **** 513905 [M::ha_hist_line] 33: * 501327 [M::ha_hist_line] 34: **** 507579 [M::ha_hist_line] 35: ** 525956 [M::ha_hist_line] 36: **** 557081 [M::ha_hist_line] 37: *** 600158 [M::ha_hist_line] 38: * 650312 [M::ha_hist_line] 39: *** 710233 [M::ha_hist_line] 40: **** 766249 [M::ha_hist_line] 41: ** 828821 [M::ha_hist_line] 42: **** 891061 [M::ha_hist_line] 43: * 944576 [M::ha_hist_line] 44: ***** 992679 [M::ha_hist_line] 45: * 1025881 [M::ha_hist_line] 46: *** 1049236 [M::ha_hist_line] 47: **** 1062125 [M::ha_hist_line] 48: * 1056117 [M::ha_hist_line] 49: ** 1036021 [M::ha_hist_line] 50: * 1012437 [M::ha_hist_line] 51: *** 969486 [M::ha_hist_line] 52: * 905024 [M::ha_hist_line] 53: ***** 839514 [M::ha_hist_line] 54: **** 768075 [M::ha_hist_line] 55: ** 696862 [M::ha_hist_line] 56: ** 616218 [M::ha_hist_line] 57: * 543995 [M::ha_hist_line] 58: **** 469749 [M::ha_hist_line] 59: ** 403234 [M::ha_hist_line] 60: **** 343699 [M::ha_hist_line] 61: **** 288974 [M::ha_hist_line] 62: 240442 [M::ha_hist_line] 63: **** 199772 [M::ha_hist_line] 64: 162928 [M::ha_hist_line] 65: ***** 133472 [M::ha_hist_line] 66: ** 105987 [M::ha_hist_line] 67: **** 85208 [M::ha_hist_line] 68: ** 67834 [M::ha_hist_line] 69: * 54779 [M::ha_hist_line] 70: ** 44234 [M::ha_hist_line] 71: ** 33906 [M::ha_hist_line] 72: 27296 [M::ha_hist_line] 73: 23431 [M::ha_hist_line] 74: 19369 [M::ha_hist_line] 75: 16953 [M::ha_hist_line] 76: 14641 [M::ha_hist_line] 77: 12842 [M::ha_hist_line] 78: 11722 [M::ha_hist_line] 79: 10753 [M::ha_hist_line] 80: 10213 [M::ha_hist_line] 81: 9484 [M::ha_hist_line] 82: 9024 [M::ha_hist_line] 83: 8467 [M::ha_hist_line] 84: 8210 [M::ha_hist_line] 85: 7629 [M::ha_hist_line] 86: 7745 [M::ha_hist_line] 87: 7571 [M::ha_hist_line] 88: 7457 [M::ha_hist_line] 89: 7456 [M::ha_hist_line] 90: 7226 [M::ha_hist_line] 91: 7129 [M::ha_hist_line] 92: 6951 [M::ha_hist_line] 93: 7033 [M::ha_hist_line] 94: 7024 [M::ha_hist_line] 95: 6903 [M::ha_hist_line] 96: 6684 [M::ha_hist_line] 97: 6374 [M::ha_hist_line] 98: 6316 [M::ha_hist_line] 99: 6225 [M::ha_hist_line] 100: 6254 [M::ha_hist_line] 101: 6029 [M::ha_hist_line] 102: 5751 [M::ha_hist_line] 103: 5706 [M::ha_hist_line] 104: 5471 [M::ha_hist_line] 105: 5582 [M::ha_hist_line] 106: * 5446 [M::ha_hist_line] rest: **** 295850 [M::ha_analyze_count] left: count[23] = 869487 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::4934.07240.45] ==> counted 37731311 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1462371695 minimizers [M::ha_pt_gen::5147.50839.91] ==> indexed 1461531748 positions, counted 37731311 distinct minimizer k-mers [M::ha_assemble::6602.22050.91@46.918GB] ==> corrected reads for round 2 [M::ha_assemble] # bases: 54188266870; # corrected bases: 2145610; # recorrected bases: 57622 [M::ha_assemble] size of buffer: 11.699GB [M::yak_count] collected 1462319994 minimizers [M::ha_pt_gen::6737.66850.64] ==> counted 38171003 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 123687 [M::ha_analyze_count] highest: count[47] = 1061577 [M::ha_hist_line] 1: ** 446705 [M::ha_hist_line] 2: ** 148886 [M::ha_hist_line] 3: **** 129399 [M::ha_hist_line] 4: **** 129521 [M::ha_hist_line] 5: **** 124203 [M::ha_hist_line] 6: **** 123687 [M::ha_hist_line] 7: **** 127318 [M::ha_hist_line] 8: *** 137744 [M::ha_hist_line] 9: ** 149436 [M::ha_hist_line] 10: **** 168744 [M::ha_hist_line] 11: ** 189971 [M::ha_hist_line] 12: * 224159 [M::ha_hist_line] 13: ***** 266639 [M::ha_hist_line] 14: ** 315698 [M::ha_hist_line] 15: **** 384206 [M::ha_hist_line] 16: * 454972 [M::ha_hist_line] 17: ** 533226 [M::ha_hist_line] 18: ** 618080 [M::ha_hist_line] 19: *** 691965 [M::ha_hist_line] 20: **** 763781 [M::ha_hist_line] 21: * 812482 [M::ha_hist_line] 22: **** 847998 [M::ha_hist_line] 23: ** 869303 [M::ha_hist_line] 24: ***** 864672 [M::ha_hist_line] 25: **** 836825 [M::ha_hist_line] 26: 793776 [M::ha_hist_line] 27: ** 745449 [M::ha_hist_line] 28: *** 686452 [M::ha_hist_line] 29: * 628655 [M::ha_hist_line] 30: **** 578860 [M::ha_hist_line] 31: 544567 [M::ha_hist_line] 32: **** 514015 [M::ha_hist_line] 33: * 501360 [M::ha_hist_line] 34: **** 507268 [M::ha_hist_line] 35: ** 525685 [M::ha_hist_line] 36: **** 556742 [M::ha_hist_line] 37: **** 599702 [M::ha_hist_line] 38: *** 649827 [M::ha_hist_line] 39: * 709695 [M::ha_hist_line] 40: **** 765739 [M::ha_hist_line] 41: ** 827653 [M::ha_hist_line] 42: **** 890527 [M::ha_hist_line] 43: *** 943964 [M::ha_hist_line] 44: * 991797 [M::ha_hist_line] 45: ***** 1025844 [M::ha_hist_line] 46: * 1048792 [M::ha_hist_line] 47: **** 1061577 [M::ha_hist_line] 48: * 1056241 [M::ha_hist_line] 49: ** 1036201 [M::ha_hist_line] 50: **** 1012640 [M::ha_hist_line] 51: 970207 [M::ha_hist_line] 52: *** 905541 [M::ha_hist_line] 53: * 839733 [M::ha_hist_line] 54: **** 768706 [M::ha_hist_line] 55: ** 697564 [M::ha_hist_line] 56: ** 617143 [M::ha_hist_line] 57: ***** 544693 [M::ha_hist_line] 58: **** 470422 [M::ha_hist_line] 59: ** 403949 [M::ha_hist_line] 60: **** 344414 [M::ha_hist_line] 61: * 289573 [M::ha_hist_line] 62: **** 241099 [M::ha_hist_line] 63: 200063 [M::ha_hist_line] 64: ** 163401 [M::ha_hist_line] 65: 133952 [M::ha_hist_line] 66: ** 106357 [M::ha_hist_line] 67: **** 85372 [M::ha_hist_line] 68: ** 68114 [M::ha_hist_line] 69: * 54960 [M::ha_hist_line] 70: ** 44387 [M::ha_hist_line] 71: * 34012 [M::ha_hist_line] 72: * 27417 [M::ha_hist_line] 73: 23422 [M::ha_hist_line] 74: 19479 [M::ha_hist_line] 75: * 16947 [M::ha_hist_line] 76: 14533 [M::ha_hist_line] 77: 12871 [M::ha_hist_line] 78: 11674 [M::ha_hist_line] 79: 10727 [M::ha_hist_line] 80: 10224 [M::ha_hist_line] 81: 9643 [M::ha_hist_line] 82: 9014 [M::ha_hist_line] 83: 8517 [M::ha_hist_line] 84: 8104 [M::ha_hist_line] 85: 7679 [M::ha_hist_line] 86: 7796 [M::ha_hist_line] 87: 7593 [M::ha_hist_line] 88: 7410 [M::ha_hist_line] 89: 7536 [M::ha_hist_line] 90: 7174 [M::ha_hist_line] 91: 7109 [M::ha_hist_line] 92: 7053 [M::ha_hist_line] 93: 7050 [M::ha_hist_line] 94: 6966 [M::ha_hist_line] 95: 6823 [M::ha_hist_line] 96: 6680 [M::ha_hist_line] 97: 6412 [M::ha_hist_line] 98: 6303 [M::ha_hist_line] 99: 6218 [M::ha_hist_line] 100: 6252 [M::ha_hist_line] 101: 6039 [M::ha_hist_line] 102: 5721 [M::ha_hist_line] 103: 5742 [M::ha_hist_line] 104: 5446 [M::ha_hist_line] 105: 5584 [M::ha_hist_line] 106: 5486 [M::ha_hist_line] rest: ** 296049 [M::ha_analyze_count] left: count[23] = 869303 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::6737.88250.64] ==> counted 37724298 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1462319994 minimizers [M::ha_pt_gen::6954.21249.97] ==> indexed 1461873289 positions, counted 37724298 distinct minimizer k-mers [M::ha_assemble::9507.72451.44@65.042GB] ==> corrected reads for round 3 [M::ha_assemble] # bases: 54188096343; # corrected bases: 261434; # recorrected bases: 57838 [M::ha_assemble] size of buffer: 11.726GB [M::yak_count] collected 1462314501 minimizers [M::ha_pt_gen::9660.53551.26] ==> counted 38150566 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 123617 [M::ha_analyze_count] highest: count[47] = 1061516 [M::ha_hist_line] 1: **** 427720 [M::ha_hist_line] 2: ** 148021 [M::ha_hist_line] 3: **** 129152 [M::ha_hist_line] 4: **** 129352 [M::ha_hist_line] 5: **** 124126 [M::ha_hist_line] 6: **** 123617 [M::ha_hist_line] 7: **** 127367 [M::ha_hist_line] 8: * 137661 [M::ha_hist_line] 9: ** 149406 [M::ha_hist_line] 10: **** 168773 [M::ha_hist_line] 11: ** 189912 [M::ha_hist_line] 12: ***** 224241 [M::ha_hist_line] 13: * 266565 [M::ha_hist_line] 14: ** 315598 [M::ha_hist_line] 15: **** 384237 [M::ha_hist_line] 16: *** 454923 [M::ha_hist_line] 17: ** 533310 [M::ha_hist_line] 18: ** 617980 [M::ha_hist_line] 19: * 691940 [M::ha_hist_line] 20: **** 763722 [M::ha_hist_line] 21: ***** 812448 [M::ha_hist_line] 22: **** 848047 [M::ha_hist_line] 23: ** 869322 [M::ha_hist_line] 24: ** 864632 [M::ha_hist_line] 25: 836877 [M::ha_hist_line] 26: *** 793784 [M::ha_hist_line] 27: ** 745397 [M::ha_hist_line] 28: * 686446 [M::ha_hist_line] 29: **** 628702 [M::ha_hist_line] 30: 578853 [M::ha_hist_line] 31: * 544556 [M::ha_hist_line] 32: **** 514014 [M::ha_hist_line] 33: * 501327 [M::ha_hist_line] 34: **** 507392 [M::ha_hist_line] 35: ** 525601 [M::ha_hist_line] 36: **** 556787 [M::ha_hist_line] 37: **** 599694 [M::ha_hist_line] 38: * 649774 [M::ha_hist_line] 39: *** 709638 [M::ha_hist_line] 40: **** 765786 [M::ha_hist_line] 41: ** 827535 [M::ha_hist_line] 42: **** 890494 [M::ha_hist_line] 43: * 944043 [M::ha_hist_line] 44: ***** 991836 [M::ha_hist_line] 45: * 1025839 [M::ha_hist_line] 46: *** 1048742 [M::ha_hist_line] 47: **** 1061516 [M::ha_hist_line] 48: **** 1056292 [M::ha_hist_line] 49: ** 1036212 [M::ha_hist_line] 50: **** 1012698 [M::ha_hist_line] 51: 970137 [M::ha_hist_line] 52: *** 905595 [M::ha_hist_line] 53: * 839770 [M::ha_hist_line] 54: **** 768707 [M::ha_hist_line] 55: ** 697600 [M::ha_hist_line] 56: ** 617135 [M::ha_hist_line] 57: ***** 544752 [M::ha_hist_line] 58: **** 470427 [M::ha_hist_line] 59: ** 403973 [M::ha_hist_line] 60: **** 344419 [M::ha_hist_line] 61: * 289606 [M::ha_hist_line] 62: **** 241088 [M::ha_hist_line] 63: 200118 [M::ha_hist_line] 64: ** 163421 [M::ha_hist_line] 65: 133969 [M::ha_hist_line] 66: ** 106388 [M::ha_hist_line] 67: **** 85320 [M::ha_hist_line] 68: ** 68114 [M::ha_hist_line] 69: * 55004 [M::ha_hist_line] 70: ** 44422 [M::ha_hist_line] 71: * 33971 [M::ha_hist_line] 72: * 27396 [M::ha_hist_line] 73: 23463 [M::ha_hist_line] 74: 19435 [M::ha_hist_line] 75: * 16968 [M::ha_hist_line] 76: 14526 [M::ha_hist_line] 77: 12884 [M::ha_hist_line] 78: 11701 [M::ha_hist_line] 79: 10659 [M::ha_hist_line] 80: 10251 [M::ha_hist_line] 81: 9621 [M::ha_hist_line] 82: 8989 [M::ha_hist_line] 83: 8549 [M::ha_hist_line] 84: 8123 [M::ha_hist_line] 85: 7677 [M::ha_hist_line] 86: 7812 [M::ha_hist_line] 87: 7568 [M::ha_hist_line] 88: 7404 [M::ha_hist_line] 89: 7565 [M::ha_hist_line] 90: 7186 [M::ha_hist_line] 91: 7116 [M::ha_hist_line] 92: 7026 [M::ha_hist_line] 93: 7026 [M::ha_hist_line] 94: 7019 [M::ha_hist_line] 95: 6803 [M::ha_hist_line] 96: 6689 [M::ha_hist_line] 97: 6403 [M::ha_hist_line] 98: 6308 [M::ha_hist_line] 99: 6201 [M::ha_hist_line] 100: 6257 [M::ha_hist_line] 101: 6056 [M::ha_hist_line] 102: 5702 [M::ha_hist_line] 103: 5714 [M::ha_hist_line] 104: 5514 [M::ha_hist_line] 105: 5551 [M::ha_hist_line] 106: 5486 [M::ha_hist_line] rest: ** 296075 [M::ha_analyze_count] left: count[23] = 869322 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::9660.77151.26] ==> counted 37722846 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 1462314501 minimizers [M::ha_pt_gen::9980.10050.90] ==> indexed 1461886781 positions, counted 37722846 distinct minimizer k-mers

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

chhylp123 commented 11 months ago

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

YanCheer commented 10 months ago

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

Thank you for reply~