Interpretation of Hifiasm results

[kiekyon]

Hi - we have generated Hifi reads from a human cancer cell line and run the initial processing on Hifiasm. The assembly size of the primary contigs from Hifiasm (estimated genome size 3.1 Gb) is 5.6 Gb, with a N50 of 1.7Mb while the Busco results indicate high duplication rate (C:95.8%[S:36.8%,D:59.0%],F:1.1%,M:3.1%,n:13780).

I wonder if there are any parameters that are specifically recommended for human cancer samples? Thanks

KK

[M::ha_analyze_count] lowest: count[10] = 6667880 [M::ha_analyze_count] highest: count[47] = 56338941 [M::ha_hist_line] 2: ***** 27473679 [M::ha_hist_line] 3: ** 12199594 [M::ha_hist_line] 4: ** 12469108 [M::ha_hist_line] 5: ** 12451682 [M::ha_hist_line] 6: **** 11379161 [M::ha_hist_line] 7: * 9744881 [M::ha_hist_line] 8: ** 8164155 [M::ha_hist_line] 9: * 7144763 [M::ha_hist_line] 10: **** 6667880 [M::ha_hist_line] 11: **** 6753116 [M::ha_hist_line] 12: * 7230217 [M::ha_hist_line] 13: ** 7986543 [M::ha_hist_line] 14: **** 9099979 [M::ha_hist_line] 15: ** 10292365 [M::ha_hist_line] 16: * 11719496 [M::ha_hist_line] 17: *** 13217994 [M::ha_hist_line] 18: ** 14797320 [M::ha_hist_line] 19: **** 15945097 [M::ha_hist_line] 20: ** 16861423 [M::ha_hist_line] 21: 17502401 [M::ha_hist_line] 22: 17723932 [M::ha_hist_line] 23: **** 17870670 [M::ha_hist_line] 24: * 17571918 [M::ha_hist_line] 25: **** 17124371 [M::ha_hist_line] 26: * 16565729 [M::ha_hist_line] 27: **** 16023608 [M::ha_hist_line] 28: **** 15579822 [M::ha_hist_line] 29: **** 15515659 [M::ha_hist_line] 30: **** 15622947 [M::ha_hist_line] 31: * 16191687 [M::ha_hist_line] 32: *** 17246352 [M::ha_hist_line] 33: * 18730311 [M::ha_hist_line] 34: ***** 20783029 [M::ha_hist_line] 35: * 23288495 [M::ha_hist_line] 36: ** 26036155 [M::ha_hist_line] 37: **** 29342922 [M::ha_hist_line] 38: ** 32851070 [M::ha_hist_line] 39: ***** 36535464 [M::ha_hist_line] 40: * 40261275 [M::ha_hist_line] 41: ** 43947872 [M::ha_hist_line] 42: **** 47375239 [M::ha_hist_line] 43: ** 50439790 [M::ha_hist_line] 44: ** 52906787 [M::ha_hist_line] 45: *** 54762352 [M::ha_hist_line] 46: *** 55801028 [M::ha_hist_line] 47: **** 56338941 [M::ha_hist_line] 48: **** 56079793 [M::ha_hist_line] 49: ** 55196663 [M::ha_hist_line] 50: **** 53857060 [M::ha_hist_line] 51: **** 51979840 [M::ha_hist_line] 52: * 49900003 [M::ha_hist_line] 53: *** 47688365 [M::ha_hist_line] 54: **** 45155732 [M::ha_hist_line] 55: **** 42712723 [M::ha_hist_line] 56: **** 40344599 [M::ha_hist_line] 57: **** 38177642 [M::ha_hist_line] 58: **** 36277344 [M::ha_hist_line] 59: ** 34705646 [M::ha_hist_line] 60: * 33294917 [M::ha_hist_line] 61: ** 32123045 [M::ha_hist_line] 62: 31099736 [M::ha_hist_line] 63: ** 30233086 [M::ha_hist_line] 64: **** 29426982 [M::ha_hist_line] 65: ** 28672191 [M::ha_hist_line] 66: 27885631 [M::ha_hist_line] 67: **** 26958760 [M::ha_hist_line] 68: ** 26039866 [M::ha_hist_line] 69: **** 25003121 [M::ha_hist_line] 70: ** 23799490 [M::ha_hist_line] 71: **** 22506480 [M::ha_hist_line] 72: ** 21067634 [M::ha_hist_line] 73: 19649227 [M::ha_hist_line] 74: **** 18217663 [M::ha_hist_line] 75: ** 16823061 [M::ha_hist_line] 76: ** 15360708 [M::ha_hist_line] 77: 14017541 [M::ha_hist_line] 78: ** 12642718 [M::ha_hist_line] 79: **** 11355795 [M::ha_hist_line] 80: ** 10189464 [M::ha_hist_line] 81: **** 9051846 [M::ha_hist_line] 82: ** 8005588 [M::ha_hist_line] 83: ** 7081460 [M::ha_hist_line] 84: 6232394 [M::ha_hist_line] 85: ** 5511262 [M::ha_hist_line] 86: * 4885049 [M::ha_hist_line] 87: ** 4347222 [M::ha_hist_line] 88: * 3902578 [M::ha_hist_line] 89: ** 3518204 [M::ha_hist_line] 90: ** 3180908 [M::ha_hist_line] 91: 2910462 [M::ha_hist_line] 92: 2693745 [M::ha_hist_line] 93: 2499333 [M::ha_hist_line] 94: 2342288 [M::ha_hist_line] 95: 2201081 [M::ha_hist_line] 96: 2080036 [M::ha_hist_line] 97: 1954532 [M::ha_hist_line] 98: 1841563 [M::ha_hist_line] 99: 1729734 [M::ha_hist_line] 100: 1629519 [M::ha_hist_line] 101: 1516697 [M::ha_hist_line] 102: 1419152 [M::ha_hist_line] 103: 1320874 [M::ha_hist_line] 104: 1246118 [M::ha_hist_line] 105: 1158950 [M::ha_hist_line] 106: 1075360 [M::ha_hist_line] 107: 992739 [M::ha_hist_line] 108: 924317 [M::ha_hist_line] 109: 856011 [M::ha_hist_line] 110: 791484 [M::ha_hist_line] 111: 729753 [M::ha_hist_line] 112: 674128 [M::ha_hist_line] 113: 620701 [M::ha_hist_line] 114: 558173 [M::ha_hist_line] 115: 510441 [M::ha_hist_line] 116: 469291 [M::ha_hist_line] 117: 441817 [M::ha_hist_line] 118: 412432 [M::ha_hist_line] 119: 383273 [M::ha_hist_line] 120: 362594 [M::ha_hist_line] 121: 337456 [M::ha_hist_line] 122: 316557 [M::ha_hist_line] 123: 303111 [M::ha_hist_line] 124: 289450 [M::ha_hist_line] 125: 284489 [M::ha_hist_line] rest: **** 19320531 [M::ha_analyze_count] left: count[23] = 17870670 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 47; peak_het: 23 [M::ha_ct_shrink::2986.8745.38] ==> counted 6874631 distinct minimizer k-mers [M::ha_ft_gen::2991.7905.37@49.217GB] ==> filtered out 6874631 k-mers occurring 235 or more times [M::ha_opt_update_cov] updated max_n_chain to 235 [M::yak_count] collected 794336747 minimizers [M::yak_count] collected 892337629 minimizers [M::yak_count] collected 894059257 minimizers [M::yak_count] collected 880986895 minimizers [M::yak_count] collected 955580715 minimizers [M::ha_pt_gen::4933.867*5.84] ==> counted 166797852 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[10] = 364561 [M::ha_analyze_count] highest: count[47] = 2256614 [M::ha_hist_line] 1: ****> 74922288 [M::ha_hist_line] 2: ****> 2467791 [M::ha_hist_line] 3: *** 870481 [M::ha_hist_line] 4: * 734195 [M::ha_hist_line] 5: *** 693531 [M::ha_hist_line] 6: **** 624085 [M::ha_hist_line] 7: **** 532607 [M::ha_hist_line] 8: **** 446433 [M::ha_hist_line] 9: * 390973 [M::ha_hist_line] 10: **** 364561 [M::ha_hist_line] 11: **** 365636 [M::ha_hist_line] 12: * 388055 [M::ha_hist_line] 13: *** 421863 [M::ha_hist_line] 14: * 472233 [M::ha_hist_line] 15: *** 525752 [M::ha_hist_line] 16: ** 588359 [M::ha_hist_line] 17: * 653196 [M::ha_hist_line] 18: **** 715662 [M::ha_hist_line] 19: ** 761606 [M::ha_hist_line] 20: *** 795418 [M::ha_hist_line] 21: **** 814393 [M::ha_hist_line] 22: **** 819901 [M::ha_hist_line] 23: **** 817516 [M::ha_hist_line] 24: * 799921 [M::ha_hist_line] 25: **** 774849 [M::ha_hist_line] 26: * 747591 [M::ha_hist_line] 27: **** 722445 [M::ha_hist_line] 28: 701678 [M::ha_hist_line] 29: 695999 [M::ha_hist_line] 30: * 699229 [M::ha_hist_line] 31: **** 720415 [M::ha_hist_line] 32: ** 764600 [M::ha_hist_line] 33: **** 822817 [M::ha_hist_line] 34: **** 906419 [M::ha_hist_line] 35: *** 1005663 [M::ha_hist_line] 36: * 1115618 [M::ha_hist_line] 37: *** 1246671 [M::ha_hist_line] 38: * 1384289 [M::ha_hist_line] 39: **** 1528726 [M::ha_hist_line] 40: ** 1672920 [M::ha_hist_line] 41: **** 1812214 [M::ha_hist_line] 42: ** 1943356 [M::ha_hist_line] 43: *** 2055660 [M::ha_hist_line] 44: * 2144963 [M::ha_hist_line] 45: ** 2210490 [M::ha_hist_line] 46: ***** 2242289 [M::ha_hist_line] 47: **** 2256614 [M::ha_hist_line] 48: ** 2238289 [M::ha_hist_line] 49: 2197129 [M::ha_hist_line] 50: **** 2137441 [M::ha_hist_line] 51: 2059015 [M::ha_hist_line] 52: **** 1976034 [M::ha_hist_line] 53: **** 1881812 [M::ha_hist_line] 54: 1781965 [M::ha_hist_line] 55: **** 1686230 [M::ha_hist_line] 56: 1591569 [M::ha_hist_line] 57: *** 1508976 [M::ha_hist_line] 58: **** 1436432 [M::ha_hist_line] 59: * 1375077 [M::ha_hist_line] 60: ** 1320844 [M::ha_hist_line] 61: 1276657 [M::ha_hist_line] 62: ** 1234187 [M::ha_hist_line] 63: 1201666 [M::ha_hist_line] 64: **** 1167265 [M::ha_hist_line] 65: ** 1137540 [M::ha_hist_line] 66: ** 1103057 [M::ha_hist_line] 67: 1066178 [M::ha_hist_line] 68: ** 1027083 [M::ha_hist_line] 69: **** 982193 [M::ha_hist_line] 70: ** 933656 [M::ha_hist_line] 71: 880939 [M::ha_hist_line] 72: **** 822950 [M::ha_hist_line] 73: ** 766800 [M::ha_hist_line] 74: ** 710793 [M::ha_hist_line] 75: 654841 [M::ha_hist_line] 76: ***** 598720 [M::ha_hist_line] 77: **** 545351 [M::ha_hist_line] 78: ** 492277 [M::ha_hist_line] 79: **** 442290 [M::ha_hist_line] 80: ** 397407 [M::ha_hist_line] 81: **** 353049 [M::ha_hist_line] 82: ** 313029 [M::ha_hist_line] 83: **** 278389 [M::ha_hist_line] 84: * 247188 [M::ha_hist_line] 85: ** 219705 [M::ha_hist_line] 86: * 195975 [M::ha_hist_line] 87: ** 175713 [M::ha_hist_line] 88: * 159559 [M::ha_hist_line] 89: ** 145402 [M::ha_hist_line] 90: ** 132659 [M::ha_hist_line] 91: 122582 [M::ha_hist_line] 92: 114246 [M::ha_hist_line] 93: * 107135 [M::ha_hist_line] 94: ** 101484 [M::ha_hist_line] 95: 95979 [M::ha_hist_line] 96: 91039 [M::ha_hist_line] 97: 86125 [M::ha_hist_line] 98: 81516 [M::ha_hist_line] 99: * 76849 [M::ha_hist_line] 100: 73057 [M::ha_hist_line] 101: 68458 [M::ha_hist_line] 102: 64508 [M::ha_hist_line] 103: 61164 [M::ha_hist_line] 104: 57966 [M::ha_hist_line] 105: 54300 [M::ha_hist_line] 106: 50460 [M::ha_hist_line] 107: 47546 [M::ha_hist_line] 108: 44461 [M::ha_hist_line] 109: 41882 [M::ha_hist_line] 110: 39858 [M::ha_hist_line] 111: 36760 [M::ha_hist_line] 112: 34903 [M::ha_hist_line] 113: 32737 [M::ha_hist_line] 114: 30190 [M::ha_hist_line] 115: 28519 [M::ha_hist_line] 116: 26941 [M::ha_hist_line] 117: 25536 [M::ha_hist_line] 118: 24202 [M::ha_hist_line] 119: 23066 [M::ha_hist_line] 120: 22004 [M::ha_hist_line] 121: 21314 [M::ha_hist_line] 122: 20209 [M::ha_hist_line] 123: 19529 [M::ha_hist_line] 124: 19009 [M::ha_hist_line] 125: 18540 [M::ha_hist_line] 126: 17763 [M::ha_hist_line] 127: 17109 [M::ha_hist_line] 128: 16398 [M::ha_hist_line] 129: 15899 [M::ha_hist_line] 130: 15646 [M::ha_hist_line] 131: 15202 [M::ha_hist_line] 132: 15201 [M::ha_hist_line] 133: 14819 [M::ha_hist_line] 134: 14433 [M::ha_hist_line] 135: 14351 [M::ha_hist_line] 136: 13882 [M::ha_hist_line] 137: 13648 [M::ha_hist_line] 138: 13534 [M::ha_hist_line] 139: 13390 [M::ha_hist_line] 140: 13163 [M::ha_hist_line] 141: 12806 [M::ha_hist_line] 142: 12642 [M::ha_hist_line] 143: 12532 [M::ha_hist_line] 144: 12708 [M::ha_hist_line] 145: 12129 [M::ha_hist_line] 146: 11981 [M::ha_hist_line] 147: 11798 [M::ha_hist_line] 148: 11774 [M::ha_hist_line] 149: 11595 [M::ha_hist_line] rest: **** 584073 [M::ha_analyze_count] left: count[22] = 819901 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 47; peak_het: 22 [M::ha_ct_shrink::4934.5795.84] ==> counted 91875564 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 4417301243 minimizers [M::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::6882.8265.90] ==> indexed 4342378955 positions, counted 91875564 distinct minimizer k-mers [M::ha_assemble::33459.55713.89@83.870GB] ==> corrected reads for round 1 [M::ha_assemble] # bases: 164279769128; # corrected bases: 372902442; # recorrected bases: 340057 [M::ha_assemble] size of buffer: 3.723GB [M::yak_count] collected 4409961020 minimizers [M::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::34359.94913.85] ==> counted 95088234 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[10] = 337675 [M::ha_analyze_count] highest: count[48] = 2228366 [M::ha_hist_line] 1: ****> 6174623 [M::ha_hist_line] 2: * 325344 [M::ha_hist_line] 3: *** 477268 [M::ha_hist_line] 4: ** 585281 [M::ha_hist_line] 5: **** 615835 [M::ha_hist_line] 6: ** 576808 [M::ha_hist_line] 7: ** 499056 [M::ha_hist_line] 8: * 418825 [M::ha_hist_line] 9: **** 364934 [M::ha_hist_line] 10: * 337675 [M::ha_hist_line] 11: * 339402 [M::ha_hist_line] 12: **** 359847 [M::ha_hist_line] 13: ** 391779 [M::ha_hist_line] 14: **** 440491 [M::ha_hist_line] 15: ** 493316 [M::ha_hist_line] 16: *** 553734 [M::ha_hist_line] 17: **** 616643 [M::ha_hist_line] 18: * 686688 [M::ha_hist_line] 19: *** 735956 [M::ha_hist_line] 20: * 773479 [M::ha_hist_line] 21: **** 798765 [M::ha_hist_line] 22: **** 806090 [M::ha_hist_line] 23: **** 808451 [M::ha_hist_line] 24: **** 793817 [M::ha_hist_line] 25: * 772802 [M::ha_hist_line] 26: * 744183 [M::ha_hist_line] 27: ** 721516 [M::ha_hist_line] 28: * 689496 [M::ha_hist_line] 29: * 684877 [M::ha_hist_line] 30: ** 675332 [M::ha_hist_line] 31: * 689360 [M::ha_hist_line] 32: **** 720807 [M::ha_hist_line] 33: ** 766023 [M::ha_hist_line] 34: ** 836586 [M::ha_hist_line] 35: * 924381 [M::ha_hist_line] 36: ** 1023705 [M::ha_hist_line] 37: *** 1139315 [M::ha_hist_line] 38: * 1272832 [M::ha_hist_line] 39: *** 1410708 [M::ha_hist_line] 40: ** 1552913 [M::ha_hist_line] 41: **** 1695502 [M::ha_hist_line] 42: ** 1832703 [M::ha_hist_line] 43: **** 1953352 [M::ha_hist_line] 44: **** 2057260 [M::ha_hist_line] 45: **** 2145177 [M::ha_hist_line] 46: ** 2194044 [M::ha_hist_line] 47: **** 2225592 [M::ha_hist_line] 48: **** 2228366 [M::ha_hist_line] 49: ** 2204798 [M::ha_hist_line] 50: 2163008 [M::ha_hist_line] 51: ** 2098819 [M::ha_hist_line] 52: **** 2017518 [M::ha_hist_line] 53: 1935565 [M::ha_hist_line] 54: ***** 1839697 [M::ha_hist_line] 55: ** 1744518 [M::ha_hist_line] 56: ** 1652022 [M::ha_hist_line] 57: ** 1556055 [M::ha_hist_line] 58: ** 1475853 [M::ha_hist_line] 59: * 1405846 [M::ha_hist_line] 60: **** 1345299 [M::ha_hist_line] 61: ** 1295453 [M::ha_hist_line] 62: **** 1254110 [M::ha_hist_line] 63: ** 1213844 [M::ha_hist_line] 64: * 1183502 [M::ha_hist_line] 65: **** 1153636 [M::ha_hist_line] 66: ** 1119528 [M::ha_hist_line] 67: * 1092968 [M::ha_hist_line] 68: ***** 1057441 [M::ha_hist_line] 69: ** 1020163 [M::ha_hist_line] 70: **** 978122 [M::ha_hist_line] 71: ** 931336 [M::ha_hist_line] 72: * 877408 [M::ha_hist_line] 73: ** 821006 [M::ha_hist_line] 74: 770365 [M::ha_hist_line] 75: **** 710701 [M::ha_hist_line] 76: ** 658118 [M::ha_hist_line] 77: ** 602289 [M::ha_hist_line] 78: 550067 [M::ha_hist_line] 79: ** 495214 [M::ha_hist_line] 80: **** 448637 [M::ha_hist_line] 81: ** 402590 [M::ha_hist_line] 82: **** 357875 [M::ha_hist_line] 83: ** 319564 [M::ha_hist_line] 84: ** 281907 [M::ha_hist_line] 85: 250582 [M::ha_hist_line] 86: ** 222927 [M::ha_hist_line] 87: * 199105 [M::ha_hist_line] 88: ** 179230 [M::ha_hist_line] 89: * 162694 [M::ha_hist_line] 90: * 146960 [M::ha_hist_line] 91: **** 134239 [M::ha_hist_line] 92: ** 123525 [M::ha_hist_line] 93: * 114667 [M::ha_hist_line] 94: 108213 [M::ha_hist_line] 95: 102118 [M::ha_hist_line] 96: 97655 [M::ha_hist_line] 97: 91263 [M::ha_hist_line] 98: 86839 [M::ha_hist_line] 99: 82664 [M::ha_hist_line] 100: ** 79331 [M::ha_hist_line] 101: ** 74140 [M::ha_hist_line] 102: 69687 [M::ha_hist_line] 103: 65616 [M::ha_hist_line] 104: 61354 [M::ha_hist_line] 105: 58376 [M::ha_hist_line] 106: 56382 [M::ha_hist_line] 107: 52630 [M::ha_hist_line] 108: 48495 [M::ha_hist_line] 109: 45763 [M::ha_hist_line] 110: 43444 [M::ha_hist_line] 111: 40063 [M::ha_hist_line] 112: 38866 [M::ha_hist_line] 113: 35870 [M::ha_hist_line] 114: 33764 [M::ha_hist_line] 115: 31158 [M::ha_hist_line] 116: 28809 [M::ha_hist_line] 117: 27339 [M::ha_hist_line] 118: 26332 [M::ha_hist_line] 119: 24201 [M::ha_hist_line] 120: 23940 [M::ha_hist_line] 121: 22543 [M::ha_hist_line] 122: 21448 [M::ha_hist_line] 123: 20483 [M::ha_hist_line] 124: 19851 [M::ha_hist_line] 125: 19421 [M::ha_hist_line] 126: 18581 [M::ha_hist_line] 127: 17822 [M::ha_hist_line] 128: 17539 [M::ha_hist_line] 129: 16513 [M::ha_hist_line] 130: 16197 [M::ha_hist_line] 131: 15918 [M::ha_hist_line] 132: 15377 [M::ha_hist_line] 133: 15120 [M::ha_hist_line] 134: 14811 [M::ha_hist_line] 135: 14419 [M::ha_hist_line] 136: 14393 [M::ha_hist_line] 137: 13753 [M::ha_hist_line] 138: 13590 [M::ha_hist_line] 139: 13195 [M::ha_hist_line] 140: 13226 [M::ha_hist_line] 141: 13073 [M::ha_hist_line] 142: 12970 [M::ha_hist_line] 143: 12804 [M::ha_hist_line] 144: 12565 [M::ha_hist_line] 145: 12711 [M::ha_hist_line] 146: 12151 [M::ha_hist_line] 147: 12398 [M::ha_hist_line] 148: 11709 [M::ha_hist_line] 149: 11319 [M::ha_hist_line] 150: 11685 [M::ha_hist_line] 151: * 11530 [M::ha_hist_line] rest: ** 585097 [M::ha_analyze_count] left: count[23] = 808451 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 48; peak_het: 23 [M::ha_ct_shrink::34360.20713.85] ==> counted 88913611 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 4409961020 minimizers [M::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::36049.07813.55] ==> indexed 4403786397 positions, counted 88913611 distinct minimizer k-mers [M::ha_assemble::58887.85514.50@88.432GB] ==> corrected reads for round 2 [M::ha_assemble] # bases: 164365387911; # corrected bases: 22188631; # recorrected bases: 224158 [M::ha_assemble] size of buffer: 3.568GB [M::yak_count] collected 4409500303 minimizers [M::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::59786.41114.47] ==> counted 90461129 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[10] = 334318 [M::ha_analyze_count] highest: count[48] = 2229306 [M::ha_hist_line] 1: **** 1689267 [M::ha_hist_line] 2: * 244081 [M::ha_hist_line] 3: **** 455754 [M::ha_hist_line] 4: ** 580943 [M::ha_hist_line] 5: ***** 611551 [M::ha_hist_line] 6: ** 573223 [M::ha_hist_line] 7: ** 495209 [M::ha_hist_line] 8: * 414886 [M::ha_hist_line] 9: **** 360937 [M::ha_hist_line] 10: * 334318 [M::ha_hist_line] 11: * 335992 [M::ha_hist_line] 12: **** 356300 [M::ha_hist_line] 13: *** 388600 [M::ha_hist_line] 14: **** 437002 [M::ha_hist_line] 15: ** 489675 [M::ha_hist_line] 16: * 551482 [M::ha_hist_line] 17: *** 612990 [M::ha_hist_line] 18: * 684208 [M::ha_hist_line] 19: *** 734612 [M::ha_hist_line] 20: * 771891 [M::ha_hist_line] 21: **** 797724 [M::ha_hist_line] 22: **** 804410 [M::ha_hist_line] 23: **** 808019 [M::ha_hist_line] 24: **** 792829 [M::ha_hist_line] 25: * 771794 [M::ha_hist_line] 26: * 743373 [M::ha_hist_line] 27: ** 720978 [M::ha_hist_line] 28: * 688434 [M::ha_hist_line] 29: * 682597 [M::ha_hist_line] 30: ** 674102 [M::ha_hist_line] 31: * 687256 [M::ha_hist_line] 32: **** 717898 [M::ha_hist_line] 33: ** 762502 [M::ha_hist_line] 34: * 832002 [M::ha_hist_line] 35: ***** 919867 [M::ha_hist_line] 36: ** 1018016 [M::ha_hist_line] 37: * 1132923 [M::ha_hist_line] 38: *** 1266688 [M::ha_hist_line] 39: * 1403658 [M::ha_hist_line] 40: *** 1547096 [M::ha_hist_line] 41: **** 1689118 [M::ha_hist_line] 42: ** 1826664 [M::ha_hist_line] 43: * 1947795 [M::ha_hist_line] 44: **** 2053869 [M::ha_hist_line] 45: **** 2141649 [M::ha_hist_line] 46: ** 2190725 [M::ha_hist_line] 47: **** 2223407 [M::ha_hist_line] 48: **** 2229306 [M::ha_hist_line] 49: ***** 2204575 [M::ha_hist_line] 50: *** 2163872 [M::ha_hist_line] 51: ** 2102106 [M::ha_hist_line] 52: * 2020162 [M::ha_hist_line] 53: **** 1938651 [M::ha_hist_line] 54: 1842724 [M::ha_hist_line] 55: ** 1746613 [M::ha_hist_line] 56: ** 1655062 [M::ha_hist_line] 57: ** 1559663 [M::ha_hist_line] 58: ** 1478154 [M::ha_hist_line] 59: *** 1407481 [M::ha_hist_line] 60: **** 1347235 [M::ha_hist_line] 61: ** 1296571 [M::ha_hist_line] 62: **** 1254706 [M::ha_hist_line] 63: ** 1213670 [M::ha_hist_line] 64: * 1184370 [M::ha_hist_line] 65: **** 1154610 [M::ha_hist_line] 66: ** 1120203 [M::ha_hist_line] 67: *** 1093580 [M::ha_hist_line] 68: **** 1060064 [M::ha_hist_line] 69: ** 1022264 [M::ha_hist_line] 70: **** 981007 [M::ha_hist_line] 71: ** 934031 [M::ha_hist_line] 72: * 880542 [M::ha_hist_line] 73: ** 823477 [M::ha_hist_line] 74: 774914 [M::ha_hist_line] 75: **** 713986 [M::ha_hist_line] 76: ** 661579 [M::ha_hist_line] 77: ** 605956 [M::ha_hist_line] 78: 554306 [M::ha_hist_line] 79: ** 498247 [M::ha_hist_line] 80: **** 451830 [M::ha_hist_line] 81: ** 406579 [M::ha_hist_line] 82: **** 360499 [M::ha_hist_line] 83: ** 321953 [M::ha_hist_line] 84: ** 284009 [M::ha_hist_line] 85: 252745 [M::ha_hist_line] 86: ** 225154 [M::ha_hist_line] 87: * 200271 [M::ha_hist_line] 88: ** 180597 [M::ha_hist_line] 89: * 163754 [M::ha_hist_line] 90: * 147999 [M::ha_hist_line] 91: **** 134701 [M::ha_hist_line] 92: ** 124390 [M::ha_hist_line] 93: * 115099 [M::ha_hist_line] 94: 108959 [M::ha_hist_line] 95: 102662 [M::ha_hist_line] 96: 98250 [M::ha_hist_line] 97: 91643 [M::ha_hist_line] 98: 87155 [M::ha_hist_line] 99: 82892 [M::ha_hist_line] 100: ** 79305 [M::ha_hist_line] 101: ** 74860 [M::ha_hist_line] 102: 70245 [M::ha_hist_line] 103: 66257 [M::ha_hist_line] 104: 61162 [M::ha_hist_line] 105: 58699 [M::ha_hist_line] 106: 56629 [M::ha_hist_line] 107: 53273 [M::ha_hist_line] 108: 48702 [M::ha_hist_line] 109: 46176 [M::ha_hist_line] 110: 43566 [M::ha_hist_line] 111: 40309 [M::ha_hist_line] 112: 38739 [M::ha_hist_line] 113: 35967 [M::ha_hist_line] 114: 34078 [M::ha_hist_line] 115: 31575 [M::ha_hist_line] 116: 28890 [M::ha_hist_line] 117: 27839 [M::ha_hist_line] 118: 26412 [M::ha_hist_line] 119: 24471 [M::ha_hist_line] 120: 24004 [M::ha_hist_line] 121: 22482 [M::ha_hist_line] 122: 21451 [M::ha_hist_line] 123: 20647 [M::ha_hist_line] 124: 19862 [M::ha_hist_line] 125: 19524 [M::ha_hist_line] 126: 18588 [M::ha_hist_line] 127: 18007 [M::ha_hist_line] 128: 17685 [M::ha_hist_line] 129: 16642 [M::ha_hist_line] 130: 16180 [M::ha_hist_line] 131: 15767 [M::ha_hist_line] 132: 15416 [M::ha_hist_line] 133: 15148 [M::ha_hist_line] 134: 14770 [M::ha_hist_line] 135: 14718 [M::ha_hist_line] 136: 14335 [M::ha_hist_line] 137: 13973 [M::ha_hist_line] 138: 13465 [M::ha_hist_line] 139: 13116 [M::ha_hist_line] 140: 13217 [M::ha_hist_line] 141: 13000 [M::ha_hist_line] 142: 12810 [M::ha_hist_line] 143: 12953 [M::ha_hist_line] 144: 12653 [M::ha_hist_line] 145: 12546 [M::ha_hist_line] 146: 12178 [M::ha_hist_line] 147: 12474 [M::ha_hist_line] 148: 11825 [M::ha_hist_line] 149: 11313 [M::ha_hist_line] 150: 11570 [M::ha_hist_line] 151: * 11524 [M::ha_hist_line] rest: ** 586990 [M::ha_analyze_count] left: count[23] = 808019 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 48; peak_het: 23 [M::ha_ct_shrink::59786.77714.47] ==> counted 88771862 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 4409500303 minimizers [M::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::60973.08514.39] ==> indexed 4407811036 positions, counted 88771862 distinct minimizer k-mers [M::ha_assemble::83908.33614.80@162.064GB] ==> corrected reads for round 3 [M::ha_assemble] # bases: 164366157643; # corrected bases: 3653380; # recorrected bases: 174143 [M::ha_assemble] size of buffer: 3.524GB [M::yak_count] collected 4409438350 minimizers [M::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::84770.31514.78] ==> counted 90160247 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[10] = 333025 [M::ha_analyze_count] highest: count[48] = 2229476 [M::ha_hist_line] 1: **** 1425403 [M::ha_hist_line] 2: ** 229746 [M::ha_hist_line] 3: **** 450839 [M::ha_hist_line] 4: ** 578517 [M::ha_hist_line] 5: ***** 609845 [M::ha_hist_line] 6: ** 571488 [M::ha_hist_line] 7: ** 493517 [M::ha_hist_line] 8: * 413637 [M::ha_hist_line] 9: **** 359951 [M::ha_hist_line] 10: 333025 [M::ha_hist_line] 11: 334620 [M::ha_hist_line] 12: **** 355070 [M::ha_hist_line] 13: * 387561 [M::ha_hist_line] 14: **** 436004 [M::ha_hist_line] 15: ** 488734 [M::ha_hist_line] 16: ***** 550750 [M::ha_hist_line] 17: * 612496 [M::ha_hist_line] 18: ***** 683583 [M::ha_hist_line] 19: * 734249 [M::ha_hist_line] 20: *** 771112 [M::ha_hist_line] 21: **** 797309 [M::ha_hist_line] 22: **** 804266 [M::ha_hist_line] 23: **** 807511 [M::ha_hist_line] 24: **** 792434 [M::ha_hist_line] 25: ** 771782 [M::ha_hist_line] 26: 743038 [M::ha_hist_line] 27: **** 720479 [M::ha_hist_line] 28: 688039 [M::ha_hist_line] 29: 682444 [M::ha_hist_line] 30: ** 673690 [M::ha_hist_line] 31: * 687275 [M::ha_hist_line] 32: **** 717556 [M::ha_hist_line] 33: ** 762193 [M::ha_hist_line] 34: *** 831600 [M::ha_hist_line] 35: * 919438 [M::ha_hist_line] 36: ** 1017449 [M::ha_hist_line] 37: *** 1132389 [M::ha_hist_line] 38: * 1266211 [M::ha_hist_line] 39: *** 1403609 [M::ha_hist_line] 40: * 1546850 [M::ha_hist_line] 41: **** 1688513 [M::ha_hist_line] 42: ** 1826582 [M::ha_hist_line] 43: *** 1947729 [M::ha_hist_line] 44: **** 2053610 [M::ha_hist_line] 45: **** 2141734 [M::ha_hist_line] 46: ** 2191238 [M::ha_hist_line] 47: **** 2223454 [M::ha_hist_line] 48: **** 2229476 [M::ha_hist_line] 49: ** 2204981 [M::ha_hist_line] 50: 2164191 [M::ha_hist_line] 51: ** 2102172 [M::ha_hist_line] 52: **** 2020308 [M::ha_hist_line] 53: 1939220 [M::ha_hist_line] 54: ***** 1842865 [M::ha_hist_line] 55: ** 1746706 [M::ha_hist_line] 56: ** 1655367 [M::ha_hist_line] 57: ** 1560032 [M::ha_hist_line] 58: ** 1478163 [M::ha_hist_line] 59: * 1407723 [M::ha_hist_line] 60: **** 1347287 [M::ha_hist_line] 61: ** 1296779 [M::ha_hist_line] 62: **** 1254856 [M::ha_hist_line] 63: ** 1213981 [M::ha_hist_line] 64: * 1184589 [M::ha_hist_line] 65: **** 1154823 [M::ha_hist_line] 66: ** 1120185 [M::ha_hist_line] 67: * 1093855 [M::ha_hist_line] 68: **** 1059996 [M::ha_hist_line] 69: ** 1022576 [M::ha_hist_line] 70: **** 981245 [M::ha_hist_line] 71: ** 934337 [M::ha_hist_line] 72: **** 880734 [M::ha_hist_line] 73: ** 823794 [M::ha_hist_line] 74: 775159 [M::ha_hist_line] 75: **** 714217 [M::ha_hist_line] 76: ** 661916 [M::ha_hist_line] 77: ** 606221 [M::ha_hist_line] 78: 554486 [M::ha_hist_line] 79: ** 498436 [M::ha_hist_line] 80: **** 451943 [M::ha_hist_line] 81: ** 406664 [M::ha_hist_line] 82: **** 360531 [M::ha_hist_line] 83: ** 322342 [M::ha_hist_line] 84: ** 283967 [M::ha_hist_line] 85: 252977 [M::ha_hist_line] 86: ** 225276 [M::ha_hist_line] 87: * 200262 [M::ha_hist_line] 88: ** 180747 [M::ha_hist_line] 89: * 163940 [M::ha_hist_line] 90: * 147979 [M::ha_hist_line] 91: **** 134699 [M::ha_hist_line] 92: ** 124401 [M::ha_hist_line] 93: * 115148 [M::ha_hist_line] 94: 109007 [M::ha_hist_line] 95: 102615 [M::ha_hist_line] 96: 98248 [M::ha_hist_line] 97: 91683 [M::ha_hist_line] 98: 87278 [M::ha_hist_line] 99: 82836 [M::ha_hist_line] 100: ** 79309 [M::ha_hist_line] 101: ** 74832 [M::ha_hist_line] 102: 70282 [M::ha_hist_line] 103: 66354 [M::ha_hist_line] 104: 61111 [M::ha_hist_line] 105: 58753 [M::ha_hist_line] 106: 56672 [M::ha_hist_line] 107: 53348 [M::ha_hist_line] 108: 48663 [M::ha_hist_line] 109: 46178 [M::ha_hist_line] 110: 43536 [M::ha_hist_line] 111: 40355 [M::ha_hist_line] 112: 38751 [M::ha_hist_line] 113: 35993 [M::ha_hist_line] 114: 34084 [M::ha_hist_line] 115: 31569 [M::ha_hist_line] 116: 28885 [M::ha_hist_line] 117: 27813 [M::ha_hist_line] 118: 26461 [M::ha_hist_line] 119: 24453 [M::ha_hist_line] 120: 24000 [M::ha_hist_line] 121: 22531 [M::ha_hist_line] 122: 21411 [M::ha_hist_line] 123: 20670 [M::ha_hist_line] 124: 19786 [M::ha_hist_line] 125: 19550 [M::ha_hist_line] 126: 18619 [M::ha_hist_line] 127: 18069 [M::ha_hist_line] 128: 17629 [M::ha_hist_line] 129: 16663 [M::ha_hist_line] 130: 16152 [M::ha_hist_line] 131: 15847 [M::ha_hist_line] 132: 15370 [M::ha_hist_line] 133: 15157 [M::ha_hist_line] 134: 14741 [M::ha_hist_line] 135: 14731 [M::ha_hist_line] 136: 14366 [M::ha_hist_line] 137: 13925 [M::ha_hist_line] 138: 13507 [M::ha_hist_line] 139: 13089 [M::ha_hist_line] 140: 13184 [M::ha_hist_line] 141: 13111 [M::ha_hist_line] 142: 12773 [M::ha_hist_line] 143: 12877 [M::ha_hist_line] 144: 12685 [M::ha_hist_line] 145: 12575 [M::ha_hist_line] 146: 12186 [M::ha_hist_line] 147: 12435 [M::ha_hist_line] 148: 11776 [M::ha_hist_line] 149: 11391 [M::ha_hist_line] 150: 11549 [M::ha_hist_line] 151: * 11563 [M::ha_hist_line] rest: ** 587139 [M::ha_analyze_count] left: count[23] = 807511 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 48; peak_het: 23 [M::ha_ct_shrink::84770.55514.78] ==> counted 88734844 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 4409438350 minimizers [M::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::85804.05414.74] ==> indexed 4408012947 positions, counted 88734844 distinct minimizer k-mers [M::ha_assemble::90759.093*14.76@177.103GB] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 513627726 [M::ha_print_ovlp_stat] # strong overlaps: 426212841 [M::ha_print_ovlp_stat] # weak overlaps: 87414885 [M::ha_print_ovlp_stat] # exact overlaps: 436096101 [M::ha_print_ovlp_stat] # inexact overlaps: 77531625 [M::ha_print_ovlp_stat] # overlaps without large indels: 508473513 [M::ha_print_ovlp_stat] # reverse overlaps: 670816908 [M::ha_opt_update_cov_min] updated max_n_chain to 240 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: 48 [M::purge_dups] purge duplication coverage threshold: 60 [M::ug_ext_gfa::] # tips::1305 Writing raw unitig GFA to disk... [M::ug_ext_gfa::] # tips::11 Writing processed unitig GFA to disk... [M::purge_dups] homozygous read coverage threshold: 48 [M::purge_dups] purge duplication coverage threshold: 60 [M::mc_solve:: # edges: 166330] [M::mc_solve_core_adv::13.347] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [40, infinity] Writing GC2_WGS2_out.hic.p_ctg.gfa to disk... [M::ha_opt_update_cov] updated max_n_chain to 240 [M::gen_trans_base_count_comp::1720.075] ==> Qualification [M::build_unitig_index::347.597] ==> Counting [M::build_unitig_index::42.330] ==> Memory allocating [M::build_unitig_index::470.063] ==> Filling pos [M::build_unitig_index::1.802] ==> Sorting pos [M::build_unitig_index::861.796] ==> HiC index has been built [M::write_hc_pt_index] Index has been written. [M::alignment_worker_pipeline::2695.951] ==> Qualification [M::dedup_hits::1.422] ==> Dedup [M::dedup_hits::0.611] ==> Dedup [M::stat] # misjoined unitigs: 18 (N50: 1039104); # corrected unitigs: 36 (N50: 738281) [M::adjust_weight_kv_u_trans_advance::1.411] [M::mc_solve:: # edges: 3666942] [M::mb_solve_core::154.512] ==> Partition [M::mc_solve_core_adv::688.674] ==> Partition [M::adjust_weight_kv_u_trans_advance::5.020] [M::mc_solve:: # edges: 3672042] [M::mb_solve_core::152.667] ==> Partition [M::mc_solve_core_adv::388.716] ==> Partition [M::adjust_weight_kv_u_trans_advance::5.028] [M::mc_solve:: # edges: 3672042] [M::mb_solve_core::152.252] ==> Partition [M::mc_solve_core_adv::238.063] ==> Partition [M::stat] # heterozygous bases: 15397003362; # homozygous bases: 278962144 [M::reduce_hamming_error_adv::4.450] # inserted edges: 92874, # fixed bubbles: 753 [M::adjust_utg_by_trio] primary contig coverage range: [40, infinity] [M::recall_arcs] # transitive arcs::744 [M::recall_arcs] # new arcs::1755758, # old arcs::979144 [M::clean_trio_untig_graph] # adjusted arcs::20 [M::adjust_utg_by_trio] primary contig coverage range: [40, infinity] [M::recall_arcs] # transitive arcs::3618 [M::recall_arcs] # new arcs::1804664, # old arcs::1019796 ERROR-set_utg_offset [M::clean_trio_untig_graph] # adjusted arcs::18 [M::output_trio_graph_joint] dedup_base::197692747, miss_base::0 Writing GC2_WGS2_out.hic.hap1.p_ctg.gfa to disk... Writing GC2_WGS2_out.hic.hap2.p_ctg.gfa to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.19.7-r598 [M::main] CMD: hifiasm -o GC2_WGS2_out --hg-size 3100m -t16 --h1 GC2_WGS2_R1.fastq.gz --h2 GC2_WGS2_R2.fastq.gz GC2_DHG033_1_A01_hifi.fastq.gz GC2_DHG033_2_B01_hifi.fastq.gz GC2_DHG033_3_C01_hifi.fastq.gz GC2_DHG033_4_D01_hifi.fastq.gz GC2_DHG033_hifi.fastq.gz [M::main] Real time: 131624.854 sec; CPU: 1439880.250 sec; Peak RSS: 349.098 GB

[chhylp123]

Everything looks fine from the log file. For cancer, it would be always better to manually curate the final contigs.

[HeQSun]

Hi @chhylp123,

I had the log error "ERROR-set_utg_offset", is it common? In my case, there was no output from hifiasm. What could be the reason?

thanks, Hequan

More log info:

[M::recall_arcs] # new arcs::70874, # old arcs::51036 ERROR-set_utg_offset ERROR-set_utg_offset [M::clean_trio_untig_graph] # adjusted arcs::4 [M::output_trio_graph_joint] dedup_base::51234249, miss_base::0 Writing ls.asm.hic.hap1.p_ctg.gfa to disk... Writing ls.asm.hic.hap2.p_ctg.gfa to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.19.8-r603

[chhylp123]

It is fine in most cases. The log file has already shown hifiasm produced ls.asm.hic.hap1.p_ctg.gfa and ls.asm.hic.hap2.p_ctg.gfa. Could you please double check these files?

[HeQSun]

Thanks. There were such files generated. So I can continue downstream analysis with such files, correct?Best,HequanOn 25. Nov 2023, at 21:45, chhylp123 @.***> wrote: It is fine in most cases. The log file has already shown hifiasm produced ls.asm.hic.hap1.p_ctg.gfa and ls.asm.hic.hap2.p_ctg.gfa. Could you please double check these files?

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