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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Assembly after individual whole-genome amplification #131

Open attrna opened 3 years ago

attrna commented 3 years ago

Hi!

I'm going to use hifiasm on HiFi data (100x coverage) from an individually amplified worm. I have a previous genome assembly version but would like to redo it with the HiFi. Also, I expect it to contain some amount of chimeric reads and very uneven coverage due to genome amplification.

I tried defaults, changed "--purge-cov", "-l0", with and w/o Hi-C data for that worm strain, but I'm getting only 20% of the expected genome size. When I map reads on the genome, I see pretty good coverage along it.

Please could you help me with the parameters that I should change in this case?

Thank you! Anastasia

chhylp123 commented 3 years ago

Could you please show what are the sizes of p_ctg.gfa/a_ctg.gfa and p_utg.gfa?

attrna commented 3 years ago

Sure!

5.6M VX0223.asm.run7.bp.hap1.p_ctg.gfa 66K VX0223.asm.run7.bp.hap1.p_ctg.noseq.gfa 1.6M VX0223.asm.run7.bp.hap2.p_ctg.gfa 15K VX0223.asm.run7.bp.hap2.p_ctg.noseq.gfa 5.6M VX0223.asm.run7.bp.p_ctg.gfa 65K VX0223.asm.run7.bp.p_ctg.noseq.gfa 5.7M VX0223.asm.run7.bp.p_utg.gfa 67K VX0223.asm.run7.bp.p_utg.noseq.gfa 5.7M VX0223.asm.run7.bp.r_utg.gfa 67K VX0223.asm.run7.bp.r_utg.noseq.gfa

chhylp123 commented 3 years ago

Thanks a lot. What's the expected genome size?

attrna commented 3 years ago

It should be around 124Mb

chhylp123 commented 3 years ago

Could you also show the log of hifiasm? Thanks again.

attrna commented 3 years ago

[M::ha_analyze_count] lowest: count[17] = 283013 [M::ha_analyze_count] highest: count[107] = 486271 [M::ha_hist_line] 2: ****> 59671349 [M::ha_hist_line] 3: ****> 23748557 [M::ha_hist_line] 4: ****> 15593415 [M::ha_hist_line] 5: ****> 6471463 [M::ha_hist_line] 6: ****> 4254465 [M::ha_hist_line] 7: ****> 2191426 [M::ha_hist_line] 8: ****> 1593932 [M::ha_hist_line] 9: ****> 930384 [M::ha_hist_line] 10: ****> 694014 [M::ha_hist_line] 11: ****> 521118 [M::ha_hist_line] 12: **** 429828 [M::ha_hist_line] 13: ** 357432 [M::ha_hist_line] 14: **** 334596 [M::ha_hist_line] 15: 315441 [M::ha_hist_line] 16: **** 290075 [M::ha_hist_line] 17: ** 283013 [M::ha_hist_line] 18: ** 284088 [M::ha_hist_line] 19: 275037 [M::ha_hist_line] 20: 277134 [M::ha_hist_line] 21: * 276786 [M::ha_hist_line] 22: ** 281059 [M::ha_hist_line] 23: *** 286580 [M::ha_hist_line] 24: **** 290626 [M::ha_hist_line] 25: * 287276 [M::ha_hist_line] 26: **** 293828 [M::ha_hist_line] 27: ** 299433 [M::ha_hist_line] 28: ** 302895 [M::ha_hist_line] 29: ***** 305595 [M::ha_hist_line] 30: **** 309213 [M::ha_hist_line] 31: **** 311992 [M::ha_hist_line] 32: * 306147 [M::ha_hist_line] 33: ** 319483 [M::ha_hist_line] 34: *** 318469 [M::ha_hist_line] 35: * 317369 [M::ha_hist_line] 36: *** 325990 [M::ha_hist_line] 37: **** 331304 [M::ha_hist_line] 38: * 336369 [M::ha_hist_line] 39: **** 331834 [M::ha_hist_line] 40: * 336698 [M::ha_hist_line] 41: ** 339498 [M::ha_hist_line] 42: * 346156 [M::ha_hist_line] 43: **** 352294 [M::ha_hist_line] 44: *** 353706 [M::ha_hist_line] 45: 366105 [M::ha_hist_line] 46: 364911 [M::ha_hist_line] 47: * 367109 [M::ha_hist_line] 48: *** 374616 [M::ha_hist_line] 49: **** 370589 [M::ha_hist_line] 50: ** 381540 [M::ha_hist_line] 51: **** 386655 [M::ha_hist_line] 52: **** 389759 [M::ha_hist_line] 53: 391509 [M::ha_hist_line] 54: 394831 [M::ha_hist_line] 55: 393623 [M::ha_hist_line] 56: 394263 [M::ha_hist_line] 57: ** 399151 [M::ha_hist_line] 58: * 395515 [M::ha_hist_line] 59: ** 398764 [M::ha_hist_line] 60: *** 401400 [M::ha_hist_line] 61: 404586 [M::ha_hist_line] 62: 402051 [M::ha_hist_line] 63: **** 410838 [M::ha_hist_line] 64: 413565 [M::ha_hist_line] 65: 413468 [M::ha_hist_line] 66: 411441 [M::ha_hist_line] 67: 414041 [M::ha_hist_line] 68: ** 420365 [M::ha_hist_line] 69: ** 420476 [M::ha_hist_line] 70: ** 417925 [M::ha_hist_line] 71: ** 420495 [M::ha_hist_line] 72: **** 428705 [M::ha_hist_line] 73: ** 435401 [M::ha_hist_line] 74: 432910 [M::ha_hist_line] 75: 432651 [M::ha_hist_line] 76: * 431775 [M::ha_hist_line] 77: ** 437991 [M::ha_hist_line] 78: ** 439246 [M::ha_hist_line] 79: *** 444073 [M::ha_hist_line] 80: **** 447176 [M::ha_hist_line] 81: **** 449689 [M::ha_hist_line] 82: ** 455668 [M::ha_hist_line] 83: ** 458114 [M::ha_hist_line] 84: ** 458705 [M::ha_hist_line] 85: * 460194 [M::ha_hist_line] 86: ** 456817 [M::ha_hist_line] 87: **** 465715 [M::ha_hist_line] 88: **** 468965 [M::ha_hist_line] 89: *** 469932 [M::ha_hist_line] 90: **** 467821 [M::ha_hist_line] 91: 470403 [M::ha_hist_line] 92: 469887 [M::ha_hist_line] 93: * 470226 [M::ha_hist_line] 94: ** 474328 [M::ha_hist_line] 95: * 473223 [M::ha_hist_line] 96: * 473487 [M::ha_hist_line] 97: ** 475064 [M::ha_hist_line] 98: ** 474538 [M::ha_hist_line] 99: ** 477157 [M::ha_hist_line] 100: ** 477238 [M::ha_hist_line] 101: ** 477272 [M::ha_hist_line] 102: ** 477168 [M::ha_hist_line] 103: *** 479517 [M::ha_hist_line] 104: * 480152 [M::ha_hist_line] 105: **** 484072 [M::ha_hist_line] 106: * 482430 [M::ha_hist_line] 107: **** 486271 [M::ha_hist_line] 108: 482300 [M::ha_hist_line] 109: 482885 [M::ha_hist_line] 110: * 482387 [M::ha_hist_line] 111: **** 484356 [M::ha_hist_line] 112: **** 485683 [M::ha_hist_line] 113: * 482453 [M::ha_hist_line] 114: ** 478840 [M::ha_hist_line] 115: **** 484437 [M::ha_hist_line] 116: **** 485815 [M::ha_hist_line] 117: * 481698 [M::ha_hist_line] 118: ** 478730 [M::ha_hist_line] 119: * 482516 [M::ha_hist_line] 120: ** 478450 [M::ha_hist_line] 121: 479195 [M::ha_hist_line] 122: 479608 [M::ha_hist_line] 123: ** 478952 [M::ha_hist_line] 124: ** 477798 [M::ha_hist_line] 125: 472800 [M::ha_hist_line] 126: 470541 [M::ha_hist_line] 127: 469738 [M::ha_hist_line] 128: 470064 [M::ha_hist_line] 129: **** 467929 [M::ha_hist_line] 130: **** 468335 [M::ha_hist_line] 131: 461884 [M::ha_hist_line] 132: 461501 [M::ha_hist_line] 133: ** 456234 [M::ha_hist_line] 134: ** 455955 [M::ha_hist_line] 135: * 454466 [M::ha_hist_line] 136: ** 455170 [M::ha_hist_line] 137: * 453368 [M::ha_hist_line] 138: * 452348 [M::ha_hist_line] 139: ** 448746 [M::ha_hist_line] 140: **** 447468 [M::ha_hist_line] 141: * 440176 [M::ha_hist_line] 142: * 434486 [M::ha_hist_line] 143: **** 438118 [M::ha_hist_line] 144: **** 430105 [M::ha_hist_line] 145: **** 427414 [M::ha_hist_line] 146: * 422604 [M::ha_hist_line] 147: **** 426009 [M::ha_hist_line] 148: * 421508 [M::ha_hist_line] 149: **** 415882 [M::ha_hist_line] 150: * 412730 [M::ha_hist_line] 151: 403750 [M::ha_hist_line] 152: 403700 [M::ha_hist_line] 153: ** 399249 [M::ha_hist_line] 154: * 391985 [M::ha_hist_line] 155: ** 388669 [M::ha_hist_line] 156: **** 389391 [M::ha_hist_line] 157: * 383049 [M::ha_hist_line] 158: ** 379837 [M::ha_hist_line] 159: 376775 [M::ha_hist_line] 160: 375132 [M::ha_hist_line] 161: **** 367815 [M::ha_hist_line] 162: * 363878 [M::ha_hist_line] 163: **** 360266 [M::ha_hist_line] 164: * 356839 [M::ha_hist_line] 165: * 353407 [M::ha_hist_line] 166: ** 350740 [M::ha_hist_line] 167: * 345711 [M::ha_hist_line] 168: ** 341765 [M::ha_hist_line] 169: ** 339812 [M::ha_hist_line] 170: 335646 [M::ha_hist_line] 171: 334648 [M::ha_hist_line] 172: **** 329817 [M::ha_hist_line] 173: * 326672 [M::ha_hist_line] 174: **** 321090 [M::ha_hist_line] 175: * 315512 [M::ha_hist_line] 176: **** 312266 [M::ha_hist_line] 177: * 306662 [M::ha_hist_line] 178: **** 303344 [M::ha_hist_line] 179: * 297276 [M::ha_hist_line] 180: * 296625 [M::ha_hist_line] 181: ** 291988 [M::ha_hist_line] 182: * 288578 [M::ha_hist_line] 183: ** 284115 [M::ha_hist_line] 184: ** 281037 [M::ha_hist_line] 185: * 275529 [M::ha_hist_line] 186: ** 271754 [M::ha_hist_line] 187: * 266477 [M::ha_hist_line] 188: ** 260720 [M::ha_hist_line] 189: 259633 [M::ha_hist_line] 190: 259700 [M::ha_hist_line] 191: **** 253161 [M::ha_hist_line] 192: 248695 [M::ha_hist_line] 193: 246006 [M::ha_hist_line] 194: 239764 [M::ha_hist_line] 195: 238345 [M::ha_hist_line] 196: **** 231473 [M::ha_hist_line] 197: * 229638 [M::ha_hist_line] 198: **** 225264 [M::ha_hist_line] 199: ** 222701 [M::ha_hist_line] 200: * 219244 [M::ha_hist_line] 201: **** 215215 [M::ha_hist_line] 202: **** 212892 [M::ha_hist_line] 203: 210034 [M::ha_hist_line] 204: 208049 [M::ha_hist_line] 205: ** 203081 [M::ha_hist_line] 206: * 197839 [M::ha_hist_line] 207: ** 194012 [M::ha_hist_line] 208: * 191960 [M::ha_hist_line] 209: 189083 [M::ha_hist_line] 210: 187716 [M::ha_hist_line] 211: ** 185187 [M::ha_hist_line] 212: 181838 [M::ha_hist_line] 213: 181968 [M::ha_hist_line] 214: **** 176948 [M::ha_hist_line] 215: **** 174835 [M::ha_hist_line] 216: 171658 [M::ha_hist_line] 217: 171994 [M::ha_hist_line] 218: ** 166905 [M::ha_hist_line] 219: ** 164499 [M::ha_hist_line] 220: 160553 [M::ha_hist_line] 221: 158448 [M::ha_hist_line] 222: **** 157710 [M::ha_hist_line] 223: 153036 [M::ha_hist_line] 224: 151071 [M::ha_hist_line] 225: ** 147196 [M::ha_hist_line] 226: ** 144127 [M::ha_hist_line] 227: 141250 [M::ha_hist_line] 228: 142176 [M::ha_hist_line] 229: **** 137833 [M::ha_hist_line] 230: **** 136086 [M::ha_hist_line] 231: * 132827 [M::ha_hist_line] 232: **** 134415 [M::ha_hist_line] 233: * 129806 [M::ha_hist_line] 234: ** 126651 [M::ha_hist_line] 235: ** 125353 [M::ha_hist_line] 236: 122427 [M::ha_hist_line] 237: 121142 [M::ha_hist_line] 238: **** 118584 [M::ha_hist_line] 239: **** 116224 [M::ha_hist_line] 240: 112807 [M::ha_hist_line] 241: 111313 [M::ha_hist_line] 242: ** 108960 [M::ha_hist_line] 243: ** 108713 [M::ha_hist_line] 244: ** 105677 [M::ha_hist_line] 245: 104349 [M::ha_hist_line] 246: 101662 [M::ha_hist_line] 247: **** 99111 [M::ha_hist_line] 248: **** 98876 [M::ha_hist_line] 249: **** 95758 [M::ha_hist_line] 250: 94441 [M::ha_hist_line] 251: 92650 [M::ha_hist_line] 252: ** 89329 [M::ha_hist_line] 253: ** 88323 [M::ha_hist_line] 254: ** 86682 [M::ha_hist_line] 255: ** 85274 [M::ha_hist_line] 256: 83542 [M::ha_hist_line] 257: 82375 [M::ha_hist_line] 258: 80368 [M::ha_hist_line] 259: 80343 [M::ha_hist_line] 260: **** 77464 [M::ha_hist_line] 261: **** 76678 [M::ha_hist_line] 262: 74986 [M::ha_hist_line] 263: 73974 [M::ha_hist_line] 264: 72510 [M::ha_hist_line] 265: 70545 [M::ha_hist_line] 266: ** 68788 [M::ha_hist_line] 267: ** 67963 [M::ha_hist_line] 268: ** 67067 [M::ha_hist_line] 269: 65267 [M::ha_hist_line] 270: 63447 [M::ha_hist_line] 271: 62455 [M::ha_hist_line] 272: 61477 [M::ha_hist_line] 273: **** 59296 [M::ha_hist_line] 274: **** 58782 [M::ha_hist_line] 275: **** 58060 [M::ha_hist_line] 276: **** 56449 [M::ha_hist_line] 277: **** 56034 [M::ha_hist_line] 278: 55088 [M::ha_hist_line] 279: 54105 [M::ha_hist_line] 280: 52227 [M::ha_hist_line] 281: 52454 [M::ha_hist_line] 282: ** 49918 [M::ha_hist_line] 283: ** 49763 [M::ha_hist_line] 284: ** 48206 [M::ha_hist_line] 285: ** 48153 [M::ha_hist_line] 286: ** 47949 [M::ha_hist_line] 287: ** 46561 [M::ha_hist_line] 288: 45708 [M::ha_hist_line] 289: 45073 [M::ha_hist_line] 290: 43740 [M::ha_hist_line] 291: 43204 [M::ha_hist_line] 292: * 42441 [M::ha_hist_line] 293: ** 41017 [M::ha_hist_line] 294: **** 40343 [M::ha_hist_line] 295: **** 40868 [M::ha_hist_line] 296: **** 39428 [M::ha_hist_line] 297: **** 37961 [M::ha_hist_line] 298: **** 39255 [M::ha_hist_line] 299: **** 38010 [M::ha_hist_line] 300: **** 36671 [M::ha_hist_line] 301: * 35811 [M::ha_hist_line] 302: 35515 [M::ha_hist_line] 303: 35871 [M::ha_hist_line] 304: 33765 [M::ha_hist_line] 305: 33197 [M::ha_hist_line] 306: * 32013 [M::ha_hist_line] 307: **** 30953 [M::ha_hist_line] 308: ** 30696 [M::ha_hist_line] 309: ** 29681 [M::ha_hist_line] 310: ** 29575 [M::ha_hist_line] 311: ** 28710 [M::ha_hist_line] 312: ** 27942 [M::ha_hist_line] 313: ** 27564 [M::ha_hist_line] 314: ** 27671 [M::ha_hist_line] 315: ** 27251 [M::ha_hist_line] 316: * 26474 [M::ha_hist_line] 317: 25671 [M::ha_hist_line] 318: 24851 [M::ha_hist_line] 319: 25003 [M::ha_hist_line] 320: 24564 [M::ha_hist_line] 321: 24262 [M::ha_hist_line] 322: 23857 [M::ha_hist_line] 323: 22760 [M::ha_hist_line] 324: 21986 [M::ha_hist_line] 325: 21205 [M::ha_hist_line] 326: 21611 [M::ha_hist_line] 327: 21150 [M::ha_hist_line] 328: 21643 [M::ha_hist_line] 329: 20317 [M::ha_hist_line] 330: 20073 [M::ha_hist_line] 331: 19307 [M::ha_hist_line] 332: 18491 [M::ha_hist_line] 333: 18416 [M::ha_hist_line] 334: 18602 [M::ha_hist_line] 335: 18524 [M::ha_hist_line] 336: 17991 [M::ha_hist_line] 337: 17880 [M::ha_hist_line] 338: 17468 [M::ha_hist_line] 339: 16676 [M::ha_hist_line] 340: 16206 [M::ha_hist_line] 341: 16032 [M::ha_hist_line] 342: 15655 [M::ha_hist_line] 343: 15804 [M::ha_hist_line] 344: 14726 [M::ha_hist_line] 345: 14858 [M::ha_hist_line] 346: 14955 [M::ha_hist_line] 347: 14809 [M::ha_hist_line] 348: 14339 [M::ha_hist_line] 349: 14388 [M::ha_hist_line] 350: 13941 [M::ha_hist_line] 351: 13990 [M::ha_hist_line] 352: 13405 [M::ha_hist_line] 353: 13027 [M::ha_hist_line] 354: 12905 [M::ha_hist_line] 355: 12549 [M::ha_hist_line] 356: 12649 [M::ha_hist_line] 357: 12608 [M::ha_hist_line] 358: 12017 [M::ha_hist_line] 359: 11946 [M::ha_hist_line] 360: 11563 [M::ha_hist_line] 361: 11786 [M::ha_hist_line] 362: 11249 [M::ha_hist_line] 363: 11057 [M::ha_hist_line] 364: 11708 [M::ha_hist_line] 365: 11093 [M::ha_hist_line] 366: 10781 [M::ha_hist_line] 367: 10784 [M::ha_hist_line] 368: 10417 [M::ha_hist_line] 369: 9974 [M::ha_hist_line] 370: 10031 [M::ha_hist_line] 371: 9501 [M::ha_hist_line] 372: 9651 [M::ha_hist_line] 373: 9535 [M::ha_hist_line] 374: 9483 [M::ha_hist_line] 375: 9328 [M::ha_hist_line] 376: 9290 [M::ha_hist_line] 377: 8760 [M::ha_hist_line] 378: 8619 [M::ha_hist_line] 379: 8575 [M::ha_hist_line] 380: 8325 [M::ha_hist_line] 381: 7962 [M::ha_hist_line] 382: 7744 [M::ha_hist_line] 383: 7463 [M::ha_hist_line] 384: 6913 [M::ha_hist_line] 385: 6676 [M::ha_hist_line] 386: 7017 [M::ha_hist_line] 387: 6959 [M::ha_hist_line] 388: 6938 [M::ha_hist_line] 389: 6760 [M::ha_hist_line] 390: 6894 [M::ha_hist_line] 391: 6568 [M::ha_hist_line] 392: 6165 [M::ha_hist_line] 393: 6294 [M::ha_hist_line] 394: 6353 [M::ha_hist_line] 395: 6143 [M::ha_hist_line] 396: 5998 [M::ha_hist_line] 397: 6079 [M::ha_hist_line] 398: 6009 [M::ha_hist_line] 399: 5722 [M::ha_hist_line] 400: 5525 [M::ha_hist_line] 401: 5442 [M::ha_hist_line] 402: 5280 [M::ha_hist_line] 403: 5478 [M::ha_hist_line] 404: 5415 [M::ha_hist_line] 405: 5672 [M::ha_hist_line] 406: 5166 [M::ha_hist_line] 407: 5139 [M::ha_hist_line] 408: 4735 [M::ha_hist_line] 409: 4861 [M::ha_hist_line] 410: 4780 [M::ha_hist_line] 411: 4723 [M::ha_hist_line] 412: 4465 [M::ha_hist_line] 413: 4378 [M::ha_hist_line] 414: 4506 [M::ha_hist_line] 415: 4223 [M::ha_hist_line] 416: 4191 [M::ha_hist_line] 417: 4070 [M::ha_hist_line] 418: 4142 [M::ha_hist_line] 419: 4098 [M::ha_hist_line] 420: 4062 [M::ha_hist_line] 421: 4042 [M::ha_hist_line] 422: 3766 [M::ha_hist_line] 423: 3844 [M::ha_hist_line] 424: 3849 [M::ha_hist_line] 425: 3932 [M::ha_hist_line] 426: 3834 [M::ha_hist_line] 427: 3400 [M::ha_hist_line] 428: 3413 [M::ha_hist_line] 429: 3284 [M::ha_hist_line] 430: 3207 [M::ha_hist_line] 431: 3091 [M::ha_hist_line] 432: 3083 [M::ha_hist_line] 433: 3017 [M::ha_hist_line] 434: 3152 [M::ha_hist_line] 435: 3078 [M::ha_hist_line] 436: 2980 [M::ha_hist_line] 437: 2848 [M::ha_hist_line] 438: 2923 [M::ha_hist_line] 439: 2775 [M::ha_hist_line] 440: 2817 [M::ha_hist_line] 441: 2986 [M::ha_hist_line] 442: 3026 [M::ha_hist_line] 443: 2743 [M::ha_hist_line] 444: 2710 [M::ha_hist_line] 445: 2977 [M::ha_hist_line] 446: 2700 [M::ha_hist_line] 447: 2631 [M::ha_hist_line] 448: 2556 [M::ha_hist_line] 449: * 2611 [M::ha_hist_line] rest: ***** 265228 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 107; peak_het: -1 [M::ha_ft_gen::339.9943.47@19.708GB] ==> filtered out 134943 k-mers occurring 535 or more times [M::ha_opt_update_cov] updated max_n_chain to 535 [M::ha_pt_gen::578.4473.27] ==> counted 18509808 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[23] = 12187 [M::ha_analyze_count] highest: count[106] = 19198 [M::ha_hist_line] 1: ****> 9703014 [M::ha_hist_line] 2: ****> 2671378 [M::ha_hist_line] 3: ****> 1115448 [M::ha_hist_line] 4: ****> 735913 [M::ha_hist_line] 5: ****> 333581 [M::ha_hist_line] 6: ****> 222711 [M::ha_hist_line] 7: ****> 125044 [M::ha_hist_line] 8: ****> 90967 [M::ha_hist_line] 9: ****> 57056 [M::ha_hist_line] 10: ****> 42426 [M::ha_hist_line] 11: ****> 31866 [M::ha_hist_line] 12: ****> 25738 [M::ha_hist_line] 13: ****> 20804 [M::ha_hist_line] 14: *** 18250 [M::ha_hist_line] 15: * 16410 [M::ha_hist_line] 16: **** 14748 [M::ha_hist_line] 17: 13971 [M::ha_hist_line] 18: ** 13408 [M::ha_hist_line] 19: * 12569 [M::ha_hist_line] 20: ** 12295 [M::ha_hist_line] 21: **** 12262 [M::ha_hist_line] 22: **** 12218 [M::ha_hist_line] 23: * 12187 [M::ha_hist_line] 24: **** 12348 [M::ha_hist_line] 25: **** 12201 [M::ha_hist_line] 26: **** 12317 [M::ha_hist_line] 27: * 12430 [M::ha_hist_line] 28: ** 12631 [M::ha_hist_line] 29: * 12573 [M::ha_hist_line] 30: ** 12584 [M::ha_hist_line] 31: ** 12702 [M::ha_hist_line] 32: * 12564 [M::ha_hist_line] 33: ***** 13156 [M::ha_hist_line] 34: 12810 [M::ha_hist_line] 35: 12879 [M::ha_hist_line] 36: * 13323 [M::ha_hist_line] 37: ** 13344 [M::ha_hist_line] 38: ** 13481 [M::ha_hist_line] 39: ** 13529 [M::ha_hist_line] 40: ** 13521 [M::ha_hist_line] 41: **** 13788 [M::ha_hist_line] 42: **** 13797 [M::ha_hist_line] 43: ** 14227 [M::ha_hist_line] 44: *** 14490 [M::ha_hist_line] 45: ** 14780 [M::ha_hist_line] 46: 14437 [M::ha_hist_line] 47: * 14722 [M::ha_hist_line] 48: *** 15078 [M::ha_hist_line] 49: * 14877 [M::ha_hist_line] 50: **** 15303 [M::ha_hist_line] 51: ** 15649 [M::ha_hist_line] 52: ***** 15518 [M::ha_hist_line] 53: * 15604 [M::ha_hist_line] 54: ** 15709 [M::ha_hist_line] 55: ** 15725 [M::ha_hist_line] 56: ** 15714 [M::ha_hist_line] 57: **** 16072 [M::ha_hist_line] 58: ** 15769 [M::ha_hist_line] 59: ** 15816 [M::ha_hist_line] 60: *** 15994 [M::ha_hist_line] 61: **** 16118 [M::ha_hist_line] 62: 15935 [M::ha_hist_line] 63: 16004 [M::ha_hist_line] 64: ** 16605 [M::ha_hist_line] 65: 16408 [M::ha_hist_line] 66: 16371 [M::ha_hist_line] 67: * 16395 [M::ha_hist_line] 68: *** 16785 [M::ha_hist_line] 69: **** 16870 [M::ha_hist_line] 70: 16608 [M::ha_hist_line] 71: 16762 [M::ha_hist_line] 72: * 17121 [M::ha_hist_line] 73: ** 17220 [M::ha_hist_line] 74: * 17163 [M::ha_hist_line] 75: ** 17260 [M::ha_hist_line] 76: ** 17306 [M::ha_hist_line] 77: ** 17352 [M::ha_hist_line] 78: * 17438 [M::ha_hist_line] 79: **** 17578 [M::ha_hist_line] 80: *** 17824 [M::ha_hist_line] 81: * 17880 [M::ha_hist_line] 82: ** 18013 [M::ha_hist_line] 83: *** 18156 [M::ha_hist_line] 84: * 18324 [M::ha_hist_line] 85: **** 18357 [M::ha_hist_line] 86: * 18176 [M::ha_hist_line] 87: **** 18483 [M::ha_hist_line] 88: * 18685 [M::ha_hist_line] 89: **** 18341 [M::ha_hist_line] 90: **** 18367 [M::ha_hist_line] 91: ** 18726 [M::ha_hist_line] 92: ** 18869 [M::ha_hist_line] 93: ** 18838 [M::ha_hist_line] 94: ** 18889 [M::ha_hist_line] 95: ** 18724 [M::ha_hist_line] 96: * 18543 [M::ha_hist_line] 97: ** 19002 [M::ha_hist_line] 98: 18672 [M::ha_hist_line] 99: 18917 [M::ha_hist_line] 100: 18927 [M::ha_hist_line] 101: 19025 [M::ha_hist_line] 102: 19059 [M::ha_hist_line] 103: ** 18867 [M::ha_hist_line] 104: * 19017 [M::ha_hist_line] 105: **** 19104 [M::ha_hist_line] 106: **** 19198 [M::ha_hist_line] 107: * 19101 [M::ha_hist_line] 108: 19074 [M::ha_hist_line] 109: 19048 [M::ha_hist_line] 110: ** 18863 [M::ha_hist_line] 111: ** 18845 [M::ha_hist_line] 112: **** 19175 [M::ha_hist_line] 113: **** 19151 [M::ha_hist_line] 114: ** 18802 [M::ha_hist_line] 115: * 19086 [M::ha_hist_line] 116: **** 19126 [M::ha_hist_line] 117: * 19098 [M::ha_hist_line] 118: * 18718 [M::ha_hist_line] 119: ** 18813 [M::ha_hist_line] 120: ** 18766 [M::ha_hist_line] 121: ** 18850 [M::ha_hist_line] 122: ** 18749 [M::ha_hist_line] 123: * 18544 [M::ha_hist_line] 124: ** 18752 [M::ha_hist_line] 125: **** 18425 [M::ha_hist_line] 126: **** 18434 [M::ha_hist_line] 127: * 18254 [M::ha_hist_line] 128: **** 18370 [M::ha_hist_line] 129: **** 18450 [M::ha_hist_line] 130: * 18316 [M::ha_hist_line] 131: ** 18088 [M::ha_hist_line] 132: ** 17960 [M::ha_hist_line] 133: 17884 [M::ha_hist_line] 134: 17771 [M::ha_hist_line] 135: * 17772 [M::ha_hist_line] 136: ** 17729 [M::ha_hist_line] 137: **** 17735 [M::ha_hist_line] 138: * 17487 [M::ha_hist_line] 139: ** 17308 [M::ha_hist_line] 140: ** 17367 [M::ha_hist_line] 141: **** 16922 [M::ha_hist_line] 142: **** 16901 [M::ha_hist_line] 143: **** 16914 [M::ha_hist_line] 144: * 16624 [M::ha_hist_line] 145: **** 16481 [M::ha_hist_line] 146: ** 16494 [M::ha_hist_line] 147: ** 16487 [M::ha_hist_line] 148: * 16244 [M::ha_hist_line] 149: **** 16033 [M::ha_hist_line] 150: **** 16050 [M::ha_hist_line] 151: ** 15814 [M::ha_hist_line] 152: **** 15393 [M::ha_hist_line] 153: **** 15400 [M::ha_hist_line] 154: 15155 [M::ha_hist_line] 155: 15161 [M::ha_hist_line] 156: ** 15041 [M::ha_hist_line] 157: **** 14667 [M::ha_hist_line] 158: **** 14594 [M::ha_hist_line] 159: * 14398 [M::ha_hist_line] 160: **** 14255 [M::ha_hist_line] 161: * 13969 [M::ha_hist_line] 162: **** 13889 [M::ha_hist_line] 163: ** 13939 [M::ha_hist_line] 164: 13696 [M::ha_hist_line] 165: * 13300 [M::ha_hist_line] 166: ** 13410 [M::ha_hist_line] 167: * 13339 [M::ha_hist_line] 168: **** 13043 [M::ha_hist_line] 169: **** 13137 [M::ha_hist_line] 170: * 12793 [M::ha_hist_line] 171: **** 12655 [M::ha_hist_line] 172: ** 12646 [M::ha_hist_line] 173: * 12393 [M::ha_hist_line] 174: * 12164 [M::ha_hist_line] 175: ** 12198 [M::ha_hist_line] 176: ** 11855 [M::ha_hist_line] 177: **** 11599 [M::ha_hist_line] 178: * 11659 [M::ha_hist_line] 179: **** 11437 [M::ha_hist_line] 180: ** 11171 [M::ha_hist_line] 181: 11019 [M::ha_hist_line] 182: 10945 [M::ha_hist_line] 183: **** 10782 [M::ha_hist_line] 184: **** 10821 [M::ha_hist_line] 185: ** 10302 [M::ha_hist_line] 186: * 10514 [M::ha_hist_line] 187: **** 10011 [M::ha_hist_line] 188: **** 9938 [M::ha_hist_line] 189: * 9852 [M::ha_hist_line] 190: ** 9652 [M::ha_hist_line] 191: * 9727 [M::ha_hist_line] 192: **** 9310 [M::ha_hist_line] 193: * 9116 [M::ha_hist_line] 194: * 9013 [M::ha_hist_line] 195: ** 8858 [M::ha_hist_line] 196: ** 8898 [M::ha_hist_line] 197: ** 8738 [M::ha_hist_line] 198: **** 8440 [M::ha_hist_line] 199: **** 8533 [M::ha_hist_line] 200: * 8168 [M::ha_hist_line] 201: * 8295 [M::ha_hist_line] 202: **** 7997 [M::ha_hist_line] 203: * 7855 [M::ha_hist_line] 204: **** 7720 [M::ha_hist_line] 205: 7532 [M::ha_hist_line] 206: 7516 [M::ha_hist_line] 207: ** 7253 [M::ha_hist_line] 208: * 7184 [M::ha_hist_line] 209: ** 7250 [M::ha_hist_line] 210: * 7078 [M::ha_hist_line] 211: ** 7038 [M::ha_hist_line] 212: 6788 [M::ha_hist_line] 213: 6810 [M::ha_hist_line] 214: 6766 [M::ha_hist_line] 215: ** 6689 [M::ha_hist_line] 216: 6369 [M::ha_hist_line] 217: * 6387 [M::ha_hist_line] 218: ** 6072 [M::ha_hist_line] 219: **** 6114 [M::ha_hist_line] 220: * 5943 [M::ha_hist_line] 221: * 5933 [M::ha_hist_line] 222: **** 5773 [M::ha_hist_line] 223: ** 5691 [M::ha_hist_line] 224: * 5596 [M::ha_hist_line] 225: 5565 [M::ha_hist_line] 226: 5529 [M::ha_hist_line] 227: **** 5410 [M::ha_hist_line] 228: 5196 [M::ha_hist_line] 229: 5186 [M::ha_hist_line] 230: ** 5040 [M::ha_hist_line] 231: ** 4909 [M::ha_hist_line] 232: ** 4964 [M::ha_hist_line] 233: **** 4702 [M::ha_hist_line] 234: * 4735 [M::ha_hist_line] 235: **** 4650 [M::ha_hist_line] 236: * 4705 [M::ha_hist_line] 237: 4443 [M::ha_hist_line] 238: 4364 [M::ha_hist_line] 239: * 4322 [M::ha_hist_line] 240: **** 4177 [M::ha_hist_line] 241: ** 4144 [M::ha_hist_line] 242: * 4020 [M::ha_hist_line] 243: 4033 [M::ha_hist_line] 244: 4005 [M::ha_hist_line] 245: **** 3782 [M::ha_hist_line] 246: * 3683 [M::ha_hist_line] 247: **** 3785 [M::ha_hist_line] 248: * 3736 [M::ha_hist_line] 249: ** 3495 [M::ha_hist_line] 250: ** 3566 [M::ha_hist_line] 251: 3335 [M::ha_hist_line] 252: 3281 [M::ha_hist_line] 253: 3227 [M::ha_hist_line] 254: 3289 [M::ha_hist_line] 255: 3206 [M::ha_hist_line] 256: **** 3112 [M::ha_hist_line] 257: **** 2989 [M::ha_hist_line] 258: **** 3004 [M::ha_hist_line] 259: **** 3025 [M::ha_hist_line] 260: 2867 [M::ha_hist_line] 261: 2814 [M::ha_hist_line] 262: * 2791 [M::ha_hist_line] 263: **** 2645 [M::ha_hist_line] 264: ** 2650 [M::ha_hist_line] 265: ** 2593 [M::ha_hist_line] 266: * 2576 [M::ha_hist_line] 267: 2467 [M::ha_hist_line] 268: 2433 [M::ha_hist_line] 269: **** 2343 [M::ha_hist_line] 270: * 2453 [M::ha_hist_line] 271: ** 2261 [M::ha_hist_line] 272: * 2189 [M::ha_hist_line] 273: **** 2216 [M::ha_hist_line] 274: 2194 [M::ha_hist_line] 275: 2136 [M::ha_hist_line] 276: 2194 [M::ha_hist_line] 277: 2032 [M::ha_hist_line] 278: * 2077 [M::ha_hist_line] 279: **** 1950 [M::ha_hist_line] 280: ** 1924 [M::ha_hist_line] 281: * 1754 [M::ha_hist_line] 282: ** 1863 [M::ha_hist_line] 283: ** 1841 [M::ha_hist_line] 284: 1775 [M::ha_hist_line] 285: 1809 [M::ha_hist_line] 286: 1751 [M::ha_hist_line] 287: 1742 [M::ha_hist_line] 288: 1704 [M::ha_hist_line] 289: 1633 [M::ha_hist_line] 290: **** 1555 [M::ha_hist_line] 291: * 1675 [M::ha_hist_line] 292: ** 1602 [M::ha_hist_line] 293: **** 1606 [M::ha_hist_line] 294: **** 1536 [M::ha_hist_line] 295: **** 1491 [M::ha_hist_line] 296: **** 1505 [M::ha_hist_line] 297: * 1411 [M::ha_hist_line] 298: **** 1473 [M::ha_hist_line] 299: 1325 [M::ha_hist_line] 300: 1278 [M::ha_hist_line] 301: 1341 [M::ha_hist_line] 302: 1261 [M::ha_hist_line] 303: * 1283 [M::ha_hist_line] 304: ** 1217 [M::ha_hist_line] 305: * 1263 [M::ha_hist_line] 306: ** 1207 [M::ha_hist_line] 307: ** 1127 [M::ha_hist_line] 308: ** 1120 [M::ha_hist_line] 309: 1036 [M::ha_hist_line] 310: 1030 [M::ha_hist_line] 311: ** 1062 [M::ha_hist_line] 312: ** 1103 [M::ha_hist_line] 313: 971 [M::ha_hist_line] 314: 1033 [M::ha_hist_line] 315: 957 [M::ha_hist_line] 316: 955 [M::ha_hist_line] 317: 993 [M::ha_hist_line] 318: 922 [M::ha_hist_line] 319: 954 [M::ha_hist_line] 320: 932 [M::ha_hist_line] 321: * 907 [M::ha_hist_line] 322: ** 851 [M::ha_hist_line] 323: 854 [M::ha_hist_line] 324: 782 [M::ha_hist_line] 325: 775 [M::ha_hist_line] 326: 772 [M::ha_hist_line] 327: 785 [M::ha_hist_line] 328: 751 [M::ha_hist_line] 329: 763 [M::ha_hist_line] 330: 712 [M::ha_hist_line] 331: 729 [M::ha_hist_line] 332: 718 [M::ha_hist_line] 333: * 659 [M::ha_hist_line] 334: ** 696 [M::ha_hist_line] 335: * 660 [M::ha_hist_line] 336: ** 684 [M::ha_hist_line] 337: * 638 [M::ha_hist_line] 338: 660 [M::ha_hist_line] 339: 586 [M::ha_hist_line] 340: 658 [M::ha_hist_line] 341: 597 [M::ha_hist_line] 342: 543 [M::ha_hist_line] 343: 552 [M::ha_hist_line] 344: 543 [M::ha_hist_line] 345: 524 [M::ha_hist_line] 346: 537 [M::ha_hist_line] 347: 597 [M::ha_hist_line] 348: 522 [M::ha_hist_line] 349: 536 [M::ha_hist_line] 350: 528 [M::ha_hist_line] 351: 486 [M::ha_hist_line] 352: 472 [M::ha_hist_line] 353: 472 [M::ha_hist_line] 354: 487 [M::ha_hist_line] 355: 528 [M::ha_hist_line] 356: 478 [M::ha_hist_line] 357: 472 [M::ha_hist_line] 358: 456 [M::ha_hist_line] 359: 436 [M::ha_hist_line] 360: 445 [M::ha_hist_line] 361: 437 [M::ha_hist_line] 362: 467 [M::ha_hist_line] 363: 440 [M::ha_hist_line] 364: 430 [M::ha_hist_line] 365: 409 [M::ha_hist_line] 366: 405 [M::ha_hist_line] 367: 358 [M::ha_hist_line] 368: 400 [M::ha_hist_line] 369: 398 [M::ha_hist_line] 370: 394 [M::ha_hist_line] 371: 345 [M::ha_hist_line] 372: 332 [M::ha_hist_line] 373: 364 [M::ha_hist_line] 374: 337 [M::ha_hist_line] 375: 354 [M::ha_hist_line] 376: 318 [M::ha_hist_line] 377: 286 [M::ha_hist_line] 378: 313 [M::ha_hist_line] 379: 326 [M::ha_hist_line] 380: 304 [M::ha_hist_line] 381: 326 [M::ha_hist_line] 382: 277 [M::ha_hist_line] 383: 288 [M::ha_hist_line] 384: 235 [M::ha_hist_line] 385: 266 [M::ha_hist_line] 386: 233 [M::ha_hist_line] 387: 264 [M::ha_hist_line] 388: 251 [M::ha_hist_line] 389: 283 [M::ha_hist_line] 390: 249 [M::ha_hist_line] 391: 223 [M::ha_hist_line] 392: 231 [M::ha_hist_line] 393: 236 [M::ha_hist_line] 394: 247 [M::ha_hist_line] 395: 223 [M::ha_hist_line] 396: 221 [M::ha_hist_line] 397: 241 [M::ha_hist_line] 398: 209 [M::ha_hist_line] 399: 220 [M::ha_hist_line] 400: 221 [M::ha_hist_line] 401: 209 [M::ha_hist_line] 402: 189 [M::ha_hist_line] 403: 195 [M::ha_hist_line] 404: 157 [M::ha_hist_line] 405: 205 [M::ha_hist_line] 406: 199 [M::ha_hist_line] 407: 169 [M::ha_hist_line] 408: 201 [M::ha_hist_line] 409: 179 [M::ha_hist_line] 410: 175 [M::ha_hist_line] 411: 174 [M::ha_hist_line] 412: 172 [M::ha_hist_line] 413: 151 [M::ha_hist_line] 414: 155 [M::ha_hist_line] 415: 171 [M::ha_hist_line] 416: 138 [M::ha_hist_line] 417: 158 [M::ha_hist_line] 418: 162 [M::ha_hist_line] 419: 139 [M::ha_hist_line] 420: 152 [M::ha_hist_line] 421: 145 [M::ha_hist_line] 422: 149 [M::ha_hist_line] 423: 142 [M::ha_hist_line] 424: 142 [M::ha_hist_line] 425: 141 [M::ha_hist_line] 426: 130 [M::ha_hist_line] 427: 131 [M::ha_hist_line] 428: 125 [M::ha_hist_line] 429: 116 [M::ha_hist_line] 430: 132 [M::ha_hist_line] 431: 130 [M::ha_hist_line] 432: 140 [M::ha_hist_line] 433: 115 [M::ha_hist_line] 434: 113 [M::ha_hist_line] 435: 103 [M::ha_hist_line] 436: 133 [M::ha_hist_line] 437: 121 [M::ha_hist_line] 438: 101 [M::ha_hist_line] 439: 113 [M::ha_hist_line] 440: 119 [M::ha_hist_line] 441: 130 [M::ha_hist_line] 442: 98 [M::ha_hist_line] rest: 6337 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 106; peak_het: -1 [M::ha_pt_gen::643.0793.77] ==> indexed 434449067 positions [M::ha_assemble::3658.28310.52@19.708GB] ==> corrected reads for round 1 [M::ha_assemble] # bases: 16980945694; # corrected bases: 1723032; # recorrected bases: 5459 [M::ha_assemble] size of buffer: 1.252GB [M::ha_pt_gen::3709.63010.50] ==> counted 18280184 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[20] = 12230 [M::ha_analyze_count] highest: count[106] = 19152 [M::ha_hist_line] 1: **> 9518248 [M::ha_hist_line] 2: ****> 2648524 [M::ha_hist_line] 3: ****> 1105572 [M::ha_hist_line] 4: ****> 730154 [M::ha_hist_line] 5: ****> 332117 [M::ha_hist_line] 6: ****> 221251 [M::ha_hist_line] 7: ****> 124295 [M::ha_hist_line] 8: ****> 90429 [M::ha_hist_line] 9: ****> 56572 [M::ha_hist_line] 10: ****> 42087 [M::ha_hist_line] 11: ****> 31637 [M::ha_hist_line] 12: ****> 25537 [M::ha_hist_line] 13: ****> 20641 [M::ha_hist_line] 14: *** 18103 [M::ha_hist_line] 15: ** 16377 [M::ha_hist_line] 16: **** 14627 [M::ha_hist_line] 17: * 13905 [M::ha_hist_line] 18: ** 13357 [M::ha_hist_line] 19: * 12543 [M::ha_hist_line] 20: ** 12230 [M::ha_hist_line] 21: **** 12236 [M::ha_hist_line] 22: **** 12200 [M::ha_hist_line] 23: **** 12207 [M::ha_hist_line] 24: **** 12305 [M::ha_hist_line] 25: * 12147 [M::ha_hist_line] 26: **** 12302 [M::ha_hist_line] 27: * 12453 [M::ha_hist_line] 28: ** 12565 [M::ha_hist_line] 29: ** 12584 [M::ha_hist_line] 30: * 12531 [M::ha_hist_line] 31: ** 12697 [M::ha_hist_line] 32: * 12543 [M::ha_hist_line] 33: ***** 13167 [M::ha_hist_line] 34: 12805 [M::ha_hist_line] 35: 12867 [M::ha_hist_line] 36: ** 13314 [M::ha_hist_line] 37: ** 13332 [M::ha_hist_line] 38: ** 13464 [M::ha_hist_line] 39: * 13537 [M::ha_hist_line] 40: ** 13487 [M::ha_hist_line] 41: **** 13764 [M::ha_hist_line] 42: **** 13813 [M::ha_hist_line] 43: ** 14203 [M::ha_hist_line] 44: **** 14465 [M::ha_hist_line] 45: *** 14733 [M::ha_hist_line] 46: **** 14477 [M::ha_hist_line] 47: * 14685 [M::ha_hist_line] 48: *** 15045 [M::ha_hist_line] 49: ** 14854 [M::ha_hist_line] 50: **** 15352 [M::ha_hist_line] 51: 15595 [M::ha_hist_line] 52: 15527 [M::ha_hist_line] 53: * 15566 [M::ha_hist_line] 54: ** 15687 [M::ha_hist_line] 55: ** 15694 [M::ha_hist_line] 56: ** 15696 [M::ha_hist_line] 57: **** 16050 [M::ha_hist_line] 58: ** 15761 [M::ha_hist_line] 59: *** 15825 [M::ha_hist_line] 60: * 15940 [M::ha_hist_line] 61: **** 16155 [M::ha_hist_line] 62: * 15885 [M::ha_hist_line] 63: **** 16001 [M::ha_hist_line] 64: * 16578 [M::ha_hist_line] 65: **** 16419 [M::ha_hist_line] 66: * 16345 [M::ha_hist_line] 67: ** 16379 [M::ha_hist_line] 68: **** 16809 [M::ha_hist_line] 69: **** 16846 [M::ha_hist_line] 70: 16572 [M::ha_hist_line] 71: 16744 [M::ha_hist_line] 72: * 17111 [M::ha_hist_line] 73: ** 17156 [M::ha_hist_line] 74: ** 17175 [M::ha_hist_line] 75: ** 17261 [M::ha_hist_line] 76: ** 17315 [M::ha_hist_line] 77: ** 17290 [M::ha_hist_line] 78: *** 17368 [M::ha_hist_line] 79: **** 17611 [M::ha_hist_line] 80: 17743 [M::ha_hist_line] 81: 17813 [M::ha_hist_line] 82: ** 18093 [M::ha_hist_line] 83: ** 18081 [M::ha_hist_line] 84: **** 18310 [M::ha_hist_line] 85: **** 18334 [M::ha_hist_line] 86: * 18160 [M::ha_hist_line] 87: **** 18451 [M::ha_hist_line] 88: ** 18702 [M::ha_hist_line] 89: **** 18307 [M::ha_hist_line] 90: **** 18303 [M::ha_hist_line] 91: ** 18682 [M::ha_hist_line] 92: ** 18782 [M::ha_hist_line] 93: ***** 18879 [M::ha_hist_line] 94: ** 18831 [M::ha_hist_line] 95: ** 18730 [M::ha_hist_line] 96: * 18539 [M::ha_hist_line] 97: *** 18953 [M::ha_hist_line] 98: ** 18687 [M::ha_hist_line] 99: 18913 [M::ha_hist_line] 100: 18917 [M::ha_hist_line] 101: 18988 [M::ha_hist_line] 102: 19043 [M::ha_hist_line] 103: ** 18824 [M::ha_hist_line] 104: **** 19067 [M::ha_hist_line] 105: **** 19094 [M::ha_hist_line] 106: **** 19152 [M::ha_hist_line] 107: * 19003 [M::ha_hist_line] 108: **** 19080 [M::ha_hist_line] 109: **** 19073 [M::ha_hist_line] 110: ** 18809 [M::ha_hist_line] 111: * 18878 [M::ha_hist_line] 112: **** 19078 [M::ha_hist_line] 113: **** 19110 [M::ha_hist_line] 114: ** 18837 [M::ha_hist_line] 115: * 19023 [M::ha_hist_line] 116: ** 19104 [M::ha_hist_line] 117: **** 19091 [M::ha_hist_line] 118: ** 18758 [M::ha_hist_line] 119: ** 18773 [M::ha_hist_line] 120: ** 18735 [M::ha_hist_line] 121: ** 18818 [M::ha_hist_line] 122: ** 18808 [M::ha_hist_line] 123: * 18620 [M::ha_hist_line] 124: * 18589 [M::ha_hist_line] 125: ** 18479 [M::ha_hist_line] 126: **** 18431 [M::ha_hist_line] 127: * 18240 [M::ha_hist_line] 128: **** 18371 [M::ha_hist_line] 129: **** 18447 [M::ha_hist_line] 130: * 18229 [M::ha_hist_line] 131: **** 18060 [M::ha_hist_line] 132: ** 17975 [M::ha_hist_line] 133: * 17846 [M::ha_hist_line] 134: 17770 [M::ha_hist_line] 135: 17755 [M::ha_hist_line] 136: 17730 [M::ha_hist_line] 137: 17807 [M::ha_hist_line] 138: * 17466 [M::ha_hist_line] 139: **** 17188 [M::ha_hist_line] 140: ** 17296 [M::ha_hist_line] 141: * 17110 [M::ha_hist_line] 142: **** 16877 [M::ha_hist_line] 143: **** 16919 [M::ha_hist_line] 144: ** 16560 [M::ha_hist_line] 145: ** 16464 [M::ha_hist_line] 146: ** 16527 [M::ha_hist_line] 147: * 16316 [M::ha_hist_line] 148: ** 16382 [M::ha_hist_line] 149: **** 16041 [M::ha_hist_line] 150: **** 16039 [M::ha_hist_line] 151: ** 15798 [M::ha_hist_line] 152: * 15442 [M::ha_hist_line] 153: **** 15346 [M::ha_hist_line] 154: 15145 [M::ha_hist_line] 155: 15132 [M::ha_hist_line] 156: ** 15080 [M::ha_hist_line] 157: 14696 [M::ha_hist_line] 158: **** 14596 [M::ha_hist_line] 159: 14389 [M::ha_hist_line] 160: 14288 [M::ha_hist_line] 161: 14023 [M::ha_hist_line] 162: 13886 [M::ha_hist_line] 163: **** 13870 [M::ha_hist_line] 164: **** 13714 [M::ha_hist_line] 165: * 13310 [M::ha_hist_line] 166: ** 13430 [M::ha_hist_line] 167: ** 13339 [M::ha_hist_line] 168: **** 13059 [M::ha_hist_line] 169: * 13150 [M::ha_hist_line] 170: * 12776 [M::ha_hist_line] 171: **** 12676 [M::ha_hist_line] 172: ** 12587 [M::ha_hist_line] 173: * 12493 [M::ha_hist_line] 174: **** 12162 [M::ha_hist_line] 175: **** 12201 [M::ha_hist_line] 176: ** 11832 [M::ha_hist_line] 177: 11687 [M::ha_hist_line] 178: 11665 [M::ha_hist_line] 179: **** 11421 [M::ha_hist_line] 180: ** 11163 [M::ha_hist_line] 181: ** 11015 [M::ha_hist_line] 182: * 10893 [M::ha_hist_line] 183: **** 10787 [M::ha_hist_line] 184: * 10855 [M::ha_hist_line] 185: ** 10401 [M::ha_hist_line] 186: * 10499 [M::ha_hist_line] 187: **** 9967 [M::ha_hist_line] 188: **** 9969 [M::ha_hist_line] 189: **** 9883 [M::ha_hist_line] 190: * 9731 [M::ha_hist_line] 191: ** 9697 [M::ha_hist_line] 192: 9303 [M::ha_hist_line] 193: **** 9155 [M::ha_hist_line] 194: * 9057 [M::ha_hist_line] 195: **** 8885 [M::ha_hist_line] 196: ** 8862 [M::ha_hist_line] 197: ** 8726 [M::ha_hist_line] 198: * 8546 [M::ha_hist_line] 199: **** 8417 [M::ha_hist_line] 200: * 8210 [M::ha_hist_line] 201: ** 8349 [M::ha_hist_line] 202: ** 7996 [M::ha_hist_line] 203: * 7892 [M::ha_hist_line] 204: ** 7847 [M::ha_hist_line] 205: 7412 [M::ha_hist_line] 206: * 7550 [M::ha_hist_line] 207: **** 7255 [M::ha_hist_line] 208: ** 7255 [M::ha_hist_line] 209: ** 7214 [M::ha_hist_line] 210: * 7091 [M::ha_hist_line] 211: ** 7038 [M::ha_hist_line] 212: 6798 [M::ha_hist_line] 213: * 6780 [M::ha_hist_line] 214: **** 6814 [M::ha_hist_line] 215: * 6701 [M::ha_hist_line] 216: ** 6439 [M::ha_hist_line] 217: * 6359 [M::ha_hist_line] 218: ** 6093 [M::ha_hist_line] 219: **** 6107 [M::ha_hist_line] 220: * 5997 [M::ha_hist_line] 221: * 5905 [M::ha_hist_line] 222: **** 5819 [M::ha_hist_line] 223: * 5643 [M::ha_hist_line] 224: 5638 [M::ha_hist_line] 225: 5630 [M::ha_hist_line] 226: * 5509 [M::ha_hist_line] 227: ** 5362 [M::ha_hist_line] 228: * 5263 [M::ha_hist_line] 229: * 5255 [M::ha_hist_line] 230: **** 5059 [M::ha_hist_line] 231: * 4862 [M::ha_hist_line] 232: ** 4929 [M::ha_hist_line] 233: 4796 [M::ha_hist_line] 234: 4720 [M::ha_hist_line] 235: **** 4644 [M::ha_hist_line] 236: **** 4691 [M::ha_hist_line] 237: **** 4512 [M::ha_hist_line] 238: * 4387 [M::ha_hist_line] 239: **** 4272 [M::ha_hist_line] 240: ** 4290 [M::ha_hist_line] 241: * 4117 [M::ha_hist_line] 242: 4061 [M::ha_hist_line] 243: 4000 [M::ha_hist_line] 244: * 3981 [M::ha_hist_line] 245: ** 3834 [M::ha_hist_line] 246: * 3703 [M::ha_hist_line] 247: * 3712 [M::ha_hist_line] 248: **** 3775 [M::ha_hist_line] 249: * 3591 [M::ha_hist_line] 250: ** 3472 [M::ha_hist_line] 251: ** 3426 [M::ha_hist_line] 252: 3284 [M::ha_hist_line] 253: 3266 [M::ha_hist_line] 254: 3270 [M::ha_hist_line] 255: 3225 [M::ha_hist_line] 256: **** 3098 [M::ha_hist_line] 257: **** 3041 [M::ha_hist_line] 258: **** 3014 [M::ha_hist_line] 259: 2955 [M::ha_hist_line] 260: 2904 [M::ha_hist_line] 261: * 2845 [M::ha_hist_line] 262: **** 2776 [M::ha_hist_line] 263: ** 2710 [M::ha_hist_line] 264: ** 2630 [M::ha_hist_line] 265: ** 2613 [M::ha_hist_line] 266: * 2575 [M::ha_hist_line] 267: 2446 [M::ha_hist_line] 268: 2489 [M::ha_hist_line] 269: **** 2317 [M::ha_hist_line] 270: * 2429 [M::ha_hist_line] 271: ** 2363 [M::ha_hist_line] 272: * 2195 [M::ha_hist_line] 273: * 2149 [M::ha_hist_line] 274: **** 2211 [M::ha_hist_line] 275: * 2153 [M::ha_hist_line] 276: 2175 [M::ha_hist_line] 277: 2075 [M::ha_hist_line] 278: * 2072 [M::ha_hist_line] 279: **** 1956 [M::ha_hist_line] 280: ** 1949 [M::ha_hist_line] 281: * 1785 [M::ha_hist_line] 282: ** 1872 [M::ha_hist_line] 283: * 1780 [M::ha_hist_line] 284: ** 1820 [M::ha_hist_line] 285: * 1782 [M::ha_hist_line] 286: 1761 [M::ha_hist_line] 287: 1777 [M::ha_hist_line] 288: 1661 [M::ha_hist_line] 289: 1675 [M::ha_hist_line] 290: **** 1578 [M::ha_hist_line] 291: * 1640 [M::ha_hist_line] 292: ** 1601 [M::ha_hist_line] 293: **** 1625 [M::ha_hist_line] 294: **** 1536 [M::ha_hist_line] 295: **** 1498 [M::ha_hist_line] 296: **** 1521 [M::ha_hist_line] 297: * 1432 [M::ha_hist_line] 298: **** 1462 [M::ha_hist_line] 299: 1359 [M::ha_hist_line] 300: 1294 [M::ha_hist_line] 301: 1301 [M::ha_hist_line] 302: 1265 [M::ha_hist_line] 303: * 1267 [M::ha_hist_line] 304: ** 1224 [M::ha_hist_line] 305: * 1305 [M::ha_hist_line] 306: ** 1199 [M::ha_hist_line] 307: ** 1168 [M::ha_hist_line] 308: ** 1094 [M::ha_hist_line] 309: ** 1060 [M::ha_hist_line] 310: 1036 [M::ha_hist_line] 311: 1048 [M::ha_hist_line] 312: ** 1089 [M::ha_hist_line] 313: 1043 [M::ha_hist_line] 314: 1023 [M::ha_hist_line] 315: 955 [M::ha_hist_line] 316: 957 [M::ha_hist_line] 317: 982 [M::ha_hist_line] 318: 924 [M::ha_hist_line] 319: 988 [M::ha_hist_line] 320: 922 [M::ha_hist_line] 321: * 905 [M::ha_hist_line] 322: ** 860 [M::ha_hist_line] 323: 860 [M::ha_hist_line] 324: 813 [M::ha_hist_line] 325: 767 [M::ha_hist_line] 326: 774 [M::ha_hist_line] 327: 770 [M::ha_hist_line] 328: 781 [M::ha_hist_line] 329: 761 [M::ha_hist_line] 330: 700 [M::ha_hist_line] 331: 725 [M::ha_hist_line] 332: 707 [M::ha_hist_line] 333: 683 [M::ha_hist_line] 334: 686 [M::ha_hist_line] 335: * 654 [M::ha_hist_line] 336: ** 683 [M::ha_hist_line] 337: ** 664 [M::ha_hist_line] 338: 658 [M::ha_hist_line] 339: 602 [M::ha_hist_line] 340: 644 [M::ha_hist_line] 341: 595 [M::ha_hist_line] 342: 555 [M::ha_hist_line] 343: 570 [M::ha_hist_line] 344: 541 [M::ha_hist_line] 345: 529 [M::ha_hist_line] 346: 519 [M::ha_hist_line] 347: 594 [M::ha_hist_line] 348: 537 [M::ha_hist_line] 349: 557 [M::ha_hist_line] 350: 509 [M::ha_hist_line] 351: 504 [M::ha_hist_line] 352: 486 [M::ha_hist_line] 353: 474 [M::ha_hist_line] 354: 472 [M::ha_hist_line] 355: 519 [M::ha_hist_line] 356: 465 [M::ha_hist_line] 357: 474 [M::ha_hist_line] 358: 483 [M::ha_hist_line] 359: 434 [M::ha_hist_line] 360: 451 [M::ha_hist_line] 361: 457 [M::ha_hist_line] 362: 434 [M::ha_hist_line] 363: 452 [M::ha_hist_line] 364: 460 [M::ha_hist_line] 365: 422 [M::ha_hist_line] 366: 380 [M::ha_hist_line] 367: 400 [M::ha_hist_line] 368: 353 [M::ha_hist_line] 369: 417 [M::ha_hist_line] 370: 377 [M::ha_hist_line] 371: 356 [M::ha_hist_line] 372: 342 [M::ha_hist_line] 373: 364 [M::ha_hist_line] 374: 362 [M::ha_hist_line] 375: 331 [M::ha_hist_line] 376: 336 [M::ha_hist_line] 377: 279 [M::ha_hist_line] 378: 304 [M::ha_hist_line] 379: 318 [M::ha_hist_line] 380: 331 [M::ha_hist_line] 381: 314 [M::ha_hist_line] 382: 280 [M::ha_hist_line] 383: 283 [M::ha_hist_line] 384: 258 [M::ha_hist_line] 385: 273 [M::ha_hist_line] 386: 249 [M::ha_hist_line] 387: 232 [M::ha_hist_line] 388: 262 [M::ha_hist_line] 389: 263 [M::ha_hist_line] 390: 248 [M::ha_hist_line] 391: 240 [M::ha_hist_line] 392: 226 [M::ha_hist_line] 393: 260 [M::ha_hist_line] 394: 219 [M::ha_hist_line] 395: 238 [M::ha_hist_line] 396: 222 [M::ha_hist_line] 397: 229 [M::ha_hist_line] 398: 225 [M::ha_hist_line] 399: 214 [M::ha_hist_line] 400: 207 [M::ha_hist_line] 401: 229 [M::ha_hist_line] 402: 190 [M::ha_hist_line] 403: 196 [M::ha_hist_line] 404: 163 [M::ha_hist_line] 405: 185 [M::ha_hist_line] 406: 211 [M::ha_hist_line] 407: 192 [M::ha_hist_line] 408: 189 [M::ha_hist_line] 409: 186 [M::ha_hist_line] 410: 172 [M::ha_hist_line] 411: 179 [M::ha_hist_line] 412: 153 [M::ha_hist_line] 413: 173 [M::ha_hist_line] 414: 152 [M::ha_hist_line] 415: 157 [M::ha_hist_line] 416: 159 [M::ha_hist_line] 417: 144 [M::ha_hist_line] 418: 165 [M::ha_hist_line] 419: 145 [M::ha_hist_line] 420: 156 [M::ha_hist_line] 421: 146 [M::ha_hist_line] 422: 137 [M::ha_hist_line] 423: 135 [M::ha_hist_line] 424: 145 [M::ha_hist_line] 425: 153 [M::ha_hist_line] 426: 128 [M::ha_hist_line] 427: 150 [M::ha_hist_line] 428: 120 [M::ha_hist_line] 429: 126 [M::ha_hist_line] 430: 114 [M::ha_hist_line] 431: 128 [M::ha_hist_line] 432: 145 [M::ha_hist_line] 433: 115 [M::ha_hist_line] 434: 118 [M::ha_hist_line] 435: 102 [M::ha_hist_line] 436: 124 [M::ha_hist_line] 437: 134 [M::ha_hist_line] 438: 100 [M::ha_hist_line] 439: 99 [M::ha_hist_line] 440: 114 [M::ha_hist_line] 441: 131 [M::ha_hist_line] 442: 112 [M::ha_hist_line] rest: 6386 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 106; peak_het: -1 [M::ha_pt_gen::3778.47210.45] ==> indexed 434604220 positions [M::ha_assemble::6793.09211.12@19.708GB] ==> corrected reads for round 2 [M::ha_assemble] # bases: 16980518568; # corrected bases: 560473; # recorrected bases: 3032 [M::ha_assemble] size of buffer: 1.209GB [M::ha_pt_gen::6841.72111.11] ==> counted 18234620 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[22] = 12163 [M::ha_analyze_count] highest: count[106] = 19182 [M::ha_hist_line] 1: ****> 9483136 [M::ha_hist_line] 2: ****> 2643746 [M::ha_hist_line] 3: ****> 1103747 [M::ha_hist_line] 4: ****> 728411 [M::ha_hist_line] 5: ****> 331596 [M::ha_hist_line] 6: ****> 220695 [M::ha_hist_line] 7: ****> 124141 [M::ha_hist_line] 8: ****> 90175 [M::ha_hist_line] 9: ****> 56404 [M::ha_hist_line] 10: ****> 41971 [M::ha_hist_line] 11: ****> 31598 [M::ha_hist_line] 12: ****> 25488 [M::ha_hist_line] 13: ****> 20598 [M::ha_hist_line] 14: ** 18053 [M::ha_hist_line] 15: ***** 16353 [M::ha_hist_line] 16: **** 14611 [M::ha_hist_line] 17: **** 13903 [M::ha_hist_line] 18: * 13329 [M::ha_hist_line] 19: * 12521 [M::ha_hist_line] 20: ** 12254 [M::ha_hist_line] 21: **** 12229 [M::ha_hist_line] 22: * 12163 [M::ha_hist_line] 23: **** 12209 [M::ha_hist_line] 24: **** 12285 [M::ha_hist_line] 25: * 12162 [M::ha_hist_line] 26: **** 12273 [M::ha_hist_line] 27: *** 12452 [M::ha_hist_line] 28: ** 12585 [M::ha_hist_line] 29: 12558 [M::ha_hist_line] 30: 12548 [M::ha_hist_line] 31: ** 12692 [M::ha_hist_line] 32: * 12551 [M::ha_hist_line] 33: ***** 13140 [M::ha_hist_line] 34: 12807 [M::ha_hist_line] 35: 12846 [M::ha_hist_line] 36: ** 13340 [M::ha_hist_line] 37: * 13310 [M::ha_hist_line] 38: ** 13458 [M::ha_hist_line] 39: *** 13549 [M::ha_hist_line] 40: ** 13488 [M::ha_hist_line] 41: **** 13770 [M::ha_hist_line] 42: **** 13798 [M::ha_hist_line] 43: ** 14215 [M::ha_hist_line] 44: * 14463 [M::ha_hist_line] 45: *** 14735 [M::ha_hist_line] 46: * 14455 [M::ha_hist_line] 47: **** 14661 [M::ha_hist_line] 48: ***** 15062 [M::ha_hist_line] 49: * 14846 [M::ha_hist_line] 50: **** 15330 [M::ha_hist_line] 51: ***** 15606 [M::ha_hist_line] 52: 15529 [M::ha_hist_line] 53: 15557 [M::ha_hist_line] 54: ** 15651 [M::ha_hist_line] 55: ** 15711 [M::ha_hist_line] 56: ** 15680 [M::ha_hist_line] 57: **** 16069 [M::ha_hist_line] 58: ** 15762 [M::ha_hist_line] 59: 15826 [M::ha_hist_line] 60: 15954 [M::ha_hist_line] 61: **** 16115 [M::ha_hist_line] 62: 15937 [M::ha_hist_line] 63: 15981 [M::ha_hist_line] 64: ** 16545 [M::ha_hist_line] 65: ** 16410 [M::ha_hist_line] 66: 16334 [M::ha_hist_line] 67: 16361 [M::ha_hist_line] 68: **** 16839 [M::ha_hist_line] 69: **** 16816 [M::ha_hist_line] 70: ** 16539 [M::ha_hist_line] 71: **** 16787 [M::ha_hist_line] 72: 17084 [M::ha_hist_line] 73: 17164 [M::ha_hist_line] 74: * 17167 [M::ha_hist_line] 75: ** 17240 [M::ha_hist_line] 76: ** 17325 [M::ha_hist_line] 77: ** 17290 [M::ha_hist_line] 78: *** 17377 [M::ha_hist_line] 79: **** 17577 [M::ha_hist_line] 80: 17754 [M::ha_hist_line] 81: 17826 [M::ha_hist_line] 82: ** 18058 [M::ha_hist_line] 83: ** 18062 [M::ha_hist_line] 84: **** 18331 [M::ha_hist_line] 85: 18303 [M::ha_hist_line] 86: 18184 [M::ha_hist_line] 87: **** 18416 [M::ha_hist_line] 88: ** 18743 [M::ha_hist_line] 89: 18266 [M::ha_hist_line] 90: 18313 [M::ha_hist_line] 91: ** 18719 [M::ha_hist_line] 92: ** 18756 [M::ha_hist_line] 93: ** 18832 [M::ha_hist_line] 94: ** 18859 [M::ha_hist_line] 95: ** 18715 [M::ha_hist_line] 96: * 18541 [M::ha_hist_line] 97: *** 18961 [M::ha_hist_line] 98: * 18698 [M::ha_hist_line] 99: *** 18897 [M::ha_hist_line] 100: 18906 [M::ha_hist_line] 101: 18931 [M::ha_hist_line] 102: **** 19102 [M::ha_hist_line] 103: ** 18796 [M::ha_hist_line] 104: **** 19090 [M::ha_hist_line] 105: * 19042 [M::ha_hist_line] 106: **** 19182 [M::ha_hist_line] 107: * 19009 [M::ha_hist_line] 108: **** 19092 [M::ha_hist_line] 109: * 19050 [M::ha_hist_line] 110: ** 18782 [M::ha_hist_line] 111: * 18908 [M::ha_hist_line] 112: 19060 [M::ha_hist_line] 113: 19064 [M::ha_hist_line] 114: ** 18861 [M::ha_hist_line] 115: * 19016 [M::ha_hist_line] 116: **** 19139 [M::ha_hist_line] 117: * 19043 [M::ha_hist_line] 118: ** 18755 [M::ha_hist_line] 119: ** 18813 [M::ha_hist_line] 120: ** 18747 [M::ha_hist_line] 121: ** 18802 [M::ha_hist_line] 122: ** 18769 [M::ha_hist_line] 123: 18616 [M::ha_hist_line] 124: 18588 [M::ha_hist_line] 125: **** 18454 [M::ha_hist_line] 126: **** 18434 [M::ha_hist_line] 127: * 18263 [M::ha_hist_line] 128: **** 18363 [M::ha_hist_line] 129: **** 18463 [M::ha_hist_line] 130: * 18222 [M::ha_hist_line] 131: ** 18040 [M::ha_hist_line] 132: ** 17962 [M::ha_hist_line] 133: 17851 [M::ha_hist_line] 134: 17788 [M::ha_hist_line] 135: * 17759 [M::ha_hist_line] 136: **** 17693 [M::ha_hist_line] 137: * 17814 [M::ha_hist_line] 138: * 17483 [M::ha_hist_line] 139: **** 17172 [M::ha_hist_line] 140: ** 17321 [M::ha_hist_line] 141: * 17097 [M::ha_hist_line] 142: **** 16867 [M::ha_hist_line] 143: **** 16923 [M::ha_hist_line] 144: ** 16548 [M::ha_hist_line] 145: ** 16493 [M::ha_hist_line] 146: ** 16472 [M::ha_hist_line] 147: 16318 [M::ha_hist_line] 148: 16389 [M::ha_hist_line] 149: **** 16086 [M::ha_hist_line] 150: 16003 [M::ha_hist_line] 151: 15830 [M::ha_hist_line] 152: **** 15437 [M::ha_hist_line] 153: **** 15315 [M::ha_hist_line] 154: 15146 [M::ha_hist_line] 155: 15171 [M::ha_hist_line] 156: ** 15059 [M::ha_hist_line] 157: 14705 [M::ha_hist_line] 158: **** 14598 [M::ha_hist_line] 159: 14387 [M::ha_hist_line] 160: 14315 [M::ha_hist_line] 161: * 14018 [M::ha_hist_line] 162: **** 13861 [M::ha_hist_line] 163: **** 13895 [M::ha_hist_line] 164: **** 13734 [M::ha_hist_line] 165: * 13270 [M::ha_hist_line] 166: ** 13441 [M::ha_hist_line] 167: ** 13351 [M::ha_hist_line] 168: **** 13093 [M::ha_hist_line] 169: **** 13114 [M::ha_hist_line] 170: * 12795 [M::ha_hist_line] 171: **** 12690 [M::ha_hist_line] 172: ** 12601 [M::ha_hist_line] 173: * 12477 [M::ha_hist_line] 174: * 12151 [M::ha_hist_line] 175: ** 12198 [M::ha_hist_line] 176: ** 11850 [M::ha_hist_line] 177: * 11716 [M::ha_hist_line] 178: * 11639 [M::ha_hist_line] 179: **** 11434 [M::ha_hist_line] 180: ** 11145 [M::ha_hist_line] 181: ** 11039 [M::ha_hist_line] 182: * 10881 [M::ha_hist_line] 183: **** 10746 [M::ha_hist_line] 184: * 10889 [M::ha_hist_line] 185: **** 10386 [M::ha_hist_line] 186: * 10537 [M::ha_hist_line] 187: **** 9964 [M::ha_hist_line] 188: **** 9984 [M::ha_hist_line] 189: **** 9895 [M::ha_hist_line] 190: 9694 [M::ha_hist_line] 191: 9728 [M::ha_hist_line] 192: * 9312 [M::ha_hist_line] 193: ** 9172 [M::ha_hist_line] 194: * 9028 [M::ha_hist_line] 195: ** 8875 [M::ha_hist_line] 196: ** 8879 [M::ha_hist_line] 197: 8697 [M::ha_hist_line] 198: 8590 [M::ha_hist_line] 199: **** 8385 [M::ha_hist_line] 200: * 8210 [M::ha_hist_line] 201: ** 8360 [M::ha_hist_line] 202: ** 8005 [M::ha_hist_line] 203: * 7867 [M::ha_hist_line] 204: ** 7859 [M::ha_hist_line] 205: 7467 [M::ha_hist_line] 206: * 7528 [M::ha_hist_line] 207: **** 7252 [M::ha_hist_line] 208: ** 7239 [M::ha_hist_line] 209: ** 7233 [M::ha_hist_line] 210: * 7087 [M::ha_hist_line] 211: ** 7032 [M::ha_hist_line] 212: 6789 [M::ha_hist_line] 213: * 6783 [M::ha_hist_line] 214: **** 6835 [M::ha_hist_line] 215: * 6693 [M::ha_hist_line] 216: ** 6430 [M::ha_hist_line] 217: * 6406 [M::ha_hist_line] 218: ** 6112 [M::ha_hist_line] 219: **** 6055 [M::ha_hist_line] 220: * 6029 [M::ha_hist_line] 221: * 5923 [M::ha_hist_line] 222: **** 5815 [M::ha_hist_line] 223: * 5654 [M::ha_hist_line] 224: 5607 [M::ha_hist_line] 225: 5657 [M::ha_hist_line] 226: * 5487 [M::ha_hist_line] 227: ** 5358 [M::ha_hist_line] 228: * 5263 [M::ha_hist_line] 229: * 5262 [M::ha_hist_line] 230: **** 5040 [M::ha_hist_line] 231: ** 4920 [M::ha_hist_line] 232: ** 4893 [M::ha_hist_line] 233: * 4780 [M::ha_hist_line] 234: * 4773 [M::ha_hist_line] 235: ** 4627 [M::ha_hist_line] 236: **** 4686 [M::ha_hist_line] 237: **** 4538 [M::ha_hist_line] 238: * 4369 [M::ha_hist_line] 239: ** 4293 [M::ha_hist_line] 240: ** 4296 [M::ha_hist_line] 241: 4113 [M::ha_hist_line] 242: 4042 [M::ha_hist_line] 243: 4035 [M::ha_hist_line] 244: 3956 [M::ha_hist_line] 245: **** 3859 [M::ha_hist_line] 246: 3693 [M::ha_hist_line] 247: 3718 [M::ha_hist_line] 248: **** 3771 [M::ha_hist_line] 249: * 3590 [M::ha_hist_line] 250: **** 3458 [M::ha_hist_line] 251: ** 3438 [M::ha_hist_line] 252: * 3292 [M::ha_hist_line] 253: 3290 [M::ha_hist_line] 254: 3251 [M::ha_hist_line] 255: * 3219 [M::ha_hist_line] 256: ** 3131 [M::ha_hist_line] 257: **** 3014 [M::ha_hist_line] 258: **** 3039 [M::ha_hist_line] 259: * 2935 [M::ha_hist_line] 260: 2913 [M::ha_hist_line] 261: 2872 [M::ha_hist_line] 262: ** 2752 [M::ha_hist_line] 263: ** 2717 [M::ha_hist_line] 264: ** 2648 [M::ha_hist_line] 265: ** 2623 [M::ha_hist_line] 266: 2544 [M::ha_hist_line] 267: 2443 [M::ha_hist_line] 268: * 2508 [M::ha_hist_line] 269: **** 2320 [M::ha_hist_line] 270: * 2430 [M::ha_hist_line] 271: **** 2343 [M::ha_hist_line] 272: **** 2236 [M::ha_hist_line] 273: 2142 [M::ha_hist_line] 274: 2194 [M::ha_hist_line] 275: 2145 [M::ha_hist_line] 276: 2199 [M::ha_hist_line] 277: 2069 [M::ha_hist_line] 278: 2066 [M::ha_hist_line] 279: ** 1967 [M::ha_hist_line] 280: ** 1947 [M::ha_hist_line] 281: * 1799 [M::ha_hist_line] 282: ** 1846 [M::ha_hist_line] 283: * 1790 [M::ha_hist_line] 284: 1822 [M::ha_hist_line] 285: 1802 [M::ha_hist_line] 286: 1728 [M::ha_hist_line] 287: 1784 [M::ha_hist_line] 288: 1678 [M::ha_hist_line] 289: 1659 [M::ha_hist_line] 290: **** 1594 [M::ha_hist_line] 291: * 1637 [M::ha_hist_line] 292: ** 1617 [M::ha_hist_line] 293: **** 1610 [M::ha_hist_line] 294: **** 1542 [M::ha_hist_line] 295: **** 1518 [M::ha_hist_line] 296: **** 1504 [M::ha_hist_line] 297: **** 1442 [M::ha_hist_line] 298: **** 1456 [M::ha_hist_line] 299: * 1373 [M::ha_hist_line] 300: 1296 [M::ha_hist_line] 301: 1295 [M::ha_hist_line] 302: 1261 [M::ha_hist_line] 303: 1270 [M::ha_hist_line] 304: ** 1229 [M::ha_hist_line] 305: * 1303 [M::ha_hist_line] 306: **** 1203 [M::ha_hist_line] 307: ** 1159 [M::ha_hist_line] 308: ** 1099 [M::ha_hist_line] 309: ** 1072 [M::ha_hist_line] 310: * 1054 [M::ha_hist_line] 311: * 1008 [M::ha_hist_line] 312: ** 1093 [M::ha_hist_line] 313: * 1047 [M::ha_hist_line] 314: 1021 [M::ha_hist_line] 315: 968 [M::ha_hist_line] 316: 959 [M::ha_hist_line] 317: 981 [M::ha_hist_line] 318: 924 [M::ha_hist_line] 319: 974 [M::ha_hist_line] 320: 943 [M::ha_hist_line] 321: 897 [M::ha_hist_line] 322: 871 [M::ha_hist_line] 323: 865 [M::ha_hist_line] 324: 809 [M::ha_hist_line] 325: 768 [M::ha_hist_line] 326: 786 [M::ha_hist_line] 327: 776 [M::ha_hist_line] 328: 761 [M::ha_hist_line] 329: 763 [M::ha_hist_line] 330: 685 [M::ha_hist_line] 331: 737 [M::ha_hist_line] 332: 709 [M::ha_hist_line] 333: 693 [M::ha_hist_line] 334: ** 680 [M::ha_hist_line] 335: * 655 [M::ha_hist_line] 336: ** 682 [M::ha_hist_line] 337: * 671 [M::ha_hist_line] 338: 651 [M::ha_hist_line] 339: 598 [M::ha_hist_line] 340: 634 [M::ha_hist_line] 341: 608 [M::ha_hist_line] 342: 563 [M::ha_hist_line] 343: 577 [M::ha_hist_line] 344: 537 [M::ha_hist_line] 345: 527 [M::ha_hist_line] 346: 516 [M::ha_hist_line] 347: 587 [M::ha_hist_line] 348: 551 [M::ha_hist_line] 349: 538 [M::ha_hist_line] 350: 526 [M::ha_hist_line] 351: 499 [M::ha_hist_line] 352: 476 [M::ha_hist_line] 353: 472 [M::ha_hist_line] 354: 492 [M::ha_hist_line] 355: 498 [M::ha_hist_line] 356: 474 [M::ha_hist_line] 357: 459 [M::ha_hist_line] 358: 493 [M::ha_hist_line] 359: 445 [M::ha_hist_line] 360: 461 [M::ha_hist_line] 361: 444 [M::ha_hist_line] 362: 425 [M::ha_hist_line] 363: 463 [M::ha_hist_line] 364: 441 [M::ha_hist_line] 365: 436 [M::ha_hist_line] 366: 389 [M::ha_hist_line] 367: 404 [M::ha_hist_line] 368: 359 [M::ha_hist_line] 369: 397 [M::ha_hist_line] 370: 379 [M::ha_hist_line] 371: 345 [M::ha_hist_line] 372: 353 [M::ha_hist_line] 373: 372 [M::ha_hist_line] 374: 360 [M::ha_hist_line] 375: 336 [M::ha_hist_line] 376: 336 [M::ha_hist_line] 377: 274 [M::ha_hist_line] 378: 309 [M::ha_hist_line] 379: 314 [M::ha_hist_line] 380: 331 [M::ha_hist_line] 381: 323 [M::ha_hist_line] 382: 278 [M::ha_hist_line] 383: 282 [M::ha_hist_line] 384: 255 [M::ha_hist_line] 385: 267 [M::ha_hist_line] 386: 270 [M::ha_hist_line] 387: 225 [M::ha_hist_line] 388: 267 [M::ha_hist_line] 389: 266 [M::ha_hist_line] 390: 243 [M::ha_hist_line] 391: 234 [M::ha_hist_line] 392: 219 [M::ha_hist_line] 393: 259 [M::ha_hist_line] 394: 236 [M::ha_hist_line] 395: 228 [M::ha_hist_line] 396: 235 [M::ha_hist_line] 397: 226 [M::ha_hist_line] 398: 217 [M::ha_hist_line] 399: 217 [M::ha_hist_line] 400: 204 [M::ha_hist_line] 401: 232 [M::ha_hist_line] 402: 191 [M::ha_hist_line] 403: 202 [M::ha_hist_line] 404: 163 [M::ha_hist_line] 405: 183 [M::ha_hist_line] 406: 200 [M::ha_hist_line] 407: 198 [M::ha_hist_line] 408: 189 [M::ha_hist_line] 409: 184 [M::ha_hist_line] 410: 181 [M::ha_hist_line] 411: 177 [M::ha_hist_line] 412: 155 [M::ha_hist_line] 413: 168 [M::ha_hist_line] 414: 156 [M::ha_hist_line] 415: 159 [M::ha_hist_line] 416: 159 [M::ha_hist_line] 417: 142 [M::ha_hist_line] 418: 163 [M::ha_hist_line] 419: 154 [M::ha_hist_line] 420: 154 [M::ha_hist_line] 421: 147 [M::ha_hist_line] 422: 135 [M::ha_hist_line] 423: 135 [M::ha_hist_line] 424: 143 [M::ha_hist_line] 425: 140 [M::ha_hist_line] 426: 135 [M::ha_hist_line] 427: 151 [M::ha_hist_line] 428: 129 [M::ha_hist_line] 429: 124 [M::ha_hist_line] 430: 111 [M::ha_hist_line] 431: 127 [M::ha_hist_line] 432: 146 [M::ha_hist_line] 433: 122 [M::ha_hist_line] 434: 117 [M::ha_hist_line] 435: 102 [M::ha_hist_line] 436: 119 [M::ha_hist_line] 437: 135 [M::ha_hist_line] 438: 103 [M::ha_hist_line] 439: 102 [M::ha_hist_line] 440: 113 [M::ha_hist_line] 441: 132 [M::ha_hist_line] 442: 104 [M::ha_hist_line] 443: 98 [M::ha_hist_line] rest: 6303 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 106; peak_het: -1 [M::ha_pt_gen::6906.64511.09] ==> indexed 434629966 positions [M::ha_assemble::9919.05011.35@19.708GB] ==> corrected reads for round 3 [M::ha_assemble] # bases: 16980357541; # corrected bases: 146162; # recorrected bases: 1862 [M::ha_assemble] size of buffer: 1.206GB [M::ha_pt_gen::9970.07711.34] ==> counted 18222502 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[22] = 12166 [M::ha_analyze_count] highest: count[106] = 19168 [M::ha_hist_line] 1: **> 9473880 [M::ha_hist_line] 2: ****> 2642441 [M::ha_hist_line] 3: ****> 1103201 [M::ha_hist_line] 4: ****> 727977 [M::ha_hist_line] 5: ****> 331426 [M::ha_hist_line] 6: ****> 220564 [M::ha_hist_line] 7: ****> 124110 [M::ha_hist_line] 8: ****> 90098 [M::ha_hist_line] 9: ****> 56356 [M::ha_hist_line] 10: ****> 41932 [M::ha_hist_line] 11: ****> 31581 [M::ha_hist_line] 12: ****> 25476 [M::ha_hist_line] 13: ****> 20598 [M::ha_hist_line] 14: ** 18040 [M::ha_hist_line] 15: ***** 16335 [M::ha_hist_line] 16: **** 14595 [M::ha_hist_line] 17: * 13913 [M::ha_hist_line] 18: **** 13316 [M::ha_hist_line] 19: 12528 [M::ha_hist_line] 20: **** 12252 [M::ha_hist_line] 21: **** 12226 [M::ha_hist_line] 22: * 12166 [M::ha_hist_line] 23: **** 12212 [M::ha_hist_line] 24: **** 12285 [M::ha_hist_line] 25: * 12158 [M::ha_hist_line] 26: **** 12278 [M::ha_hist_line] 27: * 12451 [M::ha_hist_line] 28: ** 12581 [M::ha_hist_line] 29: * 12544 [M::ha_hist_line] 30: ** 12565 [M::ha_hist_line] 31: ** 12683 [M::ha_hist_line] 32: ** 12557 [M::ha_hist_line] 33: ** 13146 [M::ha_hist_line] 34: 12803 [M::ha_hist_line] 35: * 12857 [M::ha_hist_line] 36: ** 13350 [M::ha_hist_line] 37: *** 13300 [M::ha_hist_line] 38: ** 13450 [M::ha_hist_line] 39: * 13552 [M::ha_hist_line] 40: ** 13483 [M::ha_hist_line] 41: **** 13760 [M::ha_hist_line] 42: **** 13814 [M::ha_hist_line] 43: ** 14196 [M::ha_hist_line] 44: ***** 14468 [M::ha_hist_line] 45: ** 14735 [M::ha_hist_line] 46: 14440 [M::ha_hist_line] 47: * 14671 [M::ha_hist_line] 48: *** 15055 [M::ha_hist_line] 49: ** 14856 [M::ha_hist_line] 50: **** 15318 [M::ha_hist_line] 51: 15606 [M::ha_hist_line] 52: 15531 [M::ha_hist_line] 53: * 15554 [M::ha_hist_line] 54: ** 15646 [M::ha_hist_line] 55: ** 15707 [M::ha_hist_line] 56: ** 15680 [M::ha_hist_line] 57: **** 16068 [M::ha_hist_line] 58: ** 15780 [M::ha_hist_line] 59: ** 15808 [M::ha_hist_line] 60: *** 15968 [M::ha_hist_line] 61: **** 16125 [M::ha_hist_line] 62: 15903 [M::ha_hist_line] 63: 15994 [M::ha_hist_line] 64: ** 16539 [M::ha_hist_line] 65: ** 16421 [M::ha_hist_line] 66: 16333 [M::ha_hist_line] 67: 16358 [M::ha_hist_line] 68: **** 16846 [M::ha_hist_line] 69: **** 16808 [M::ha_hist_line] 70: ** 16531 [M::ha_hist_line] 71: **** 16791 [M::ha_hist_line] 72: * 17065 [M::ha_hist_line] 73: ** 17191 [M::ha_hist_line] 74: ** 17168 [M::ha_hist_line] 75: ** 17239 [M::ha_hist_line] 76: ** 17319 [M::ha_hist_line] 77: ** 17267 [M::ha_hist_line] 78: *** 17407 [M::ha_hist_line] 79: **** 17561 [M::ha_hist_line] 80: 17763 [M::ha_hist_line] 81: 17829 [M::ha_hist_line] 82: ** 18028 [M::ha_hist_line] 83: ** 18063 [M::ha_hist_line] 84: **** 18342 [M::ha_hist_line] 85: 18301 [M::ha_hist_line] 86: 18165 [M::ha_hist_line] 87: **** 18439 [M::ha_hist_line] 88: ** 18724 [M::ha_hist_line] 89: * 18268 [M::ha_hist_line] 90: **** 18330 [M::ha_hist_line] 91: ** 18706 [M::ha_hist_line] 92: ** 18741 [M::ha_hist_line] 93: ** 18838 [M::ha_hist_line] 94: ** 18836 [M::ha_hist_line] 95: ** 18730 [M::ha_hist_line] 96: *** 18555 [M::ha_hist_line] 97: ** 18973 [M::ha_hist_line] 98: 18678 [M::ha_hist_line] 99: 18901 [M::ha_hist_line] 100: 18889 [M::ha_hist_line] 101: * 18925 [M::ha_hist_line] 102: **** 19118 [M::ha_hist_line] 103: ** 18799 [M::ha_hist_line] 104: **** 19079 [M::ha_hist_line] 105: * 19043 [M::ha_hist_line] 106: **** 19168 [M::ha_hist_line] 107: * 19034 [M::ha_hist_line] 108: **** 19089 [M::ha_hist_line] 109: * 19042 [M::ha_hist_line] 110: ** 18759 [M::ha_hist_line] 111: * 18914 [M::ha_hist_line] 112: **** 19074 [M::ha_hist_line] 113: * 19060 [M::ha_hist_line] 114: ** 18878 [M::ha_hist_line] 115: * 19009 [M::ha_hist_line] 116: **** 19125 [M::ha_hist_line] 117: * 19031 [M::ha_hist_line] 118: ** 18765 [M::ha_hist_line] 119: ** 18811 [M::ha_hist_line] 120: ** 18754 [M::ha_hist_line] 121: ** 18800 [M::ha_hist_line] 122: ** 18786 [M::ha_hist_line] 123: 18587 [M::ha_hist_line] 124: 18586 [M::ha_hist_line] 125: **** 18436 [M::ha_hist_line] 126: **** 18449 [M::ha_hist_line] 127: * 18260 [M::ha_hist_line] 128: **** 18355 [M::ha_hist_line] 129: **** 18462 [M::ha_hist_line] 130: * 18227 [M::ha_hist_line] 131: ** 18053 [M::ha_hist_line] 132: ** 17935 [M::ha_hist_line] 133: 17857 [M::ha_hist_line] 134: 17782 [M::ha_hist_line] 135: * 17771 [M::ha_hist_line] 136: **** 17691 [M::ha_hist_line] 137: * 17805 [M::ha_hist_line] 138: * 17480 [M::ha_hist_line] 139: **** 17196 [M::ha_hist_line] 140: ** 17325 [M::ha_hist_line] 141: * 17081 [M::ha_hist_line] 142: **** 16885 [M::ha_hist_line] 143: **** 16933 [M::ha_hist_line] 144: ** 16542 [M::ha_hist_line] 145: ** 16486 [M::ha_hist_line] 146: ** 16469 [M::ha_hist_line] 147: * 16311 [M::ha_hist_line] 148: **** 16400 [M::ha_hist_line] 149: **** 16077 [M::ha_hist_line] 150: * 16003 [M::ha_hist_line] 151: * 15837 [M::ha_hist_line] 152: **** 15420 [M::ha_hist_line] 153: **** 15303 [M::ha_hist_line] 154: * 15171 [M::ha_hist_line] 155: 15168 [M::ha_hist_line] 156: 15056 [M::ha_hist_line] 157: * 14687 [M::ha_hist_line] 158: ** 14617 [M::ha_hist_line] 159: * 14370 [M::ha_hist_line] 160: ** 14315 [M::ha_hist_line] 161: 14055 [M::ha_hist_line] 162: **** 13863 [M::ha_hist_line] 163: **** 13868 [M::ha_hist_line] 164: **** 13731 [M::ha_hist_line] 165: * 13280 [M::ha_hist_line] 166: **** 13449 [M::ha_hist_line] 167: ** 13349 [M::ha_hist_line] 168: **** 13094 [M::ha_hist_line] 169: **** 13108 [M::ha_hist_line] 170: * 12806 [M::ha_hist_line] 171: ** 12693 [M::ha_hist_line] 172: ** 12588 [M::ha_hist_line] 173: ** 12489 [M::ha_hist_line] 174: 12146 [M::ha_hist_line] 175: **** 12194 [M::ha_hist_line] 176: ** 11871 [M::ha_hist_line] 177: 11701 [M::ha_hist_line] 178: 11636 [M::ha_hist_line] 179: **** 11437 [M::ha_hist_line] 180: ** 11154 [M::ha_hist_line] 181: ** 11045 [M::ha_hist_line] 182: * 10863 [M::ha_hist_line] 183: **** 10748 [M::ha_hist_line] 184: * 10898 [M::ha_hist_line] 185: ** 10364 [M::ha_hist_line] 186: * 10540 [M::ha_hist_line] 187: **** 9988 [M::ha_hist_line] 188: **** 9960 [M::ha_hist_line] 189: **** 9902 [M::ha_hist_line] 190: * 9700 [M::ha_hist_line] 191: ** 9714 [M::ha_hist_line] 192: 9328 [M::ha_hist_line] 193: **** 9169 [M::ha_hist_line] 194: * 9047 [M::ha_hist_line] 195: **** 8856 [M::ha_hist_line] 196: ** 8904 [M::ha_hist_line] 197: * 8681 [M::ha_hist_line] 198: * 8577 [M::ha_hist_line] 199: ** 8401 [M::ha_hist_line] 200: * 8205 [M::ha_hist_line] 201: **** 8362 [M::ha_hist_line] 202: ** 8014 [M::ha_hist_line] 203: 7852 [M::ha_hist_line] 204: 7866 [M::ha_hist_line] 205: 7473 [M::ha_hist_line] 206: 7538 [M::ha_hist_line] 207: ** 7250 [M::ha_hist_line] 208: ** 7241 [M::ha_hist_line] 209: ** 7247 [M::ha_hist_line] 210: 7071 [M::ha_hist_line] 211: 7018 [M::ha_hist_line] 212: **** 6809 [M::ha_hist_line] 213: * 6765 [M::ha_hist_line] 214: **** 6834 [M::ha_hist_line] 215: * 6689 [M::ha_hist_line] 216: ** 6441 [M::ha_hist_line] 217: ** 6428 [M::ha_hist_line] 218: **** 6094 [M::ha_hist_line] 219: **** 6055 [M::ha_hist_line] 220: 6029 [M::ha_hist_line] 221: 5922 [M::ha_hist_line] 222: ** 5829 [M::ha_hist_line] 223: 5653 [M::ha_hist_line] 224: 5608 [M::ha_hist_line] 225: 5648 [M::ha_hist_line] 226: 5494 [M::ha_hist_line] 227: **** 5345 [M::ha_hist_line] 228: **** 5286 [M::ha_hist_line] 229: * 5243 [M::ha_hist_line] 230: **** 5059 [M::ha_hist_line] 231: ** 4915 [M::ha_hist_line] 232: * 4885 [M::ha_hist_line] 233: 4771 [M::ha_hist_line] 234: 4787 [M::ha_hist_line] 235: **** 4618 [M::ha_hist_line] 236: **** 4695 [M::ha_hist_line] 237: **** 4518 [M::ha_hist_line] 238: * 4397 [M::ha_hist_line] 239: **** 4279 [M::ha_hist_line] 240: ** 4303 [M::ha_hist_line] 241: * 4113 [M::ha_hist_line] 242: 4044 [M::ha_hist_line] 243: 4043 [M::ha_hist_line] 244: * 3933 [M::ha_hist_line] 245: ** 3863 [M::ha_hist_line] 246: * 3693 [M::ha_hist_line] 247: * 3731 [M::ha_hist_line] 248: **** 3753 [M::ha_hist_line] 249: * 3603 [M::ha_hist_line] 250: ** 3476 [M::ha_hist_line] 251: ** 3440 [M::ha_hist_line] 252: 3288 [M::ha_hist_line] 253: 3290 [M::ha_hist_line] 254: 3247 [M::ha_hist_line] 255: 3207 [M::ha_hist_line] 256: **** 3139 [M::ha_hist_line] 257: **** 3022 [M::ha_hist_line] 258: **** 3028 [M::ha_hist_line] 259: 2933 [M::ha_hist_line] 260: 2920 [M::ha_hist_line] 261: 2868 [M::ha_hist_line] 262: 2782 [M::ha_hist_line] 263: ** 2701 [M::ha_hist_line] 264: ** 2638 [M::ha_hist_line] 265: ** 2641 [M::ha_hist_line] 266: 2536 [M::ha_hist_line] 267: 2454 [M::ha_hist_line] 268: * 2490 [M::ha_hist_line] 269: **** 2320 [M::ha_hist_line] 270: * 2444 [M::ha_hist_line] 271: **** 2338 [M::ha_hist_line] 272: **** 2239 [M::ha_hist_line] 273: 2142 [M::ha_hist_line] 274: 2190 [M::ha_hist_line] 275: * 2143 [M::ha_hist_line] 276: **** 2215 [M::ha_hist_line] 277: * 2061 [M::ha_hist_line] 278: * 2060 [M::ha_hist_line] 279: **** 1975 [M::ha_hist_line] 280: ** 1951 [M::ha_hist_line] 281: * 1791 [M::ha_hist_line] 282: ** 1853 [M::ha_hist_line] 283: 1783 [M::ha_hist_line] 284: 1819 [M::ha_hist_line] 285: 1801 [M::ha_hist_line] 286: 1738 [M::ha_hist_line] 287: 1794 [M::ha_hist_line] 288: 1664 [M::ha_hist_line] 289: * 1658 [M::ha_hist_line] 290: **** 1589 [M::ha_hist_line] 291: * 1640 [M::ha_hist_line] 292: **** 1615 [M::ha_hist_line] 293: **** 1617 [M::ha_hist_line] 294: **** 1541 [M::ha_hist_line] 295: **** 1506 [M::ha_hist_line] 296: **** 1515 [M::ha_hist_line] 297: * 1433 [M::ha_hist_line] 298: **** 1467 [M::ha_hist_line] 299: * 1381 [M::ha_hist_line] 300: 1286 [M::ha_hist_line] 301: 1301 [M::ha_hist_line] 302: 1256 [M::ha_hist_line] 303: 1254 [M::ha_hist_line] 304: ** 1243 [M::ha_hist_line] 305: * 1294 [M::ha_hist_line] 306: **** 1217 [M::ha_hist_line] 307: ** 1154 [M::ha_hist_line] 308: ** 1106 [M::ha_hist_line] 309: ** 1072 [M::ha_hist_line] 310: ** 1057 [M::ha_hist_line] 311: * 1013 [M::ha_hist_line] 312: ** 1088 [M::ha_hist_line] 313: 1039 [M::ha_hist_line] 314: 1022 [M::ha_hist_line] 315: 978 [M::ha_hist_line] 316: 955 [M::ha_hist_line] 317: 982 [M::ha_hist_line] 318: 928 [M::ha_hist_line] 319: 967 [M::ha_hist_line] 320: 945 [M::ha_hist_line] 321: 887 [M::ha_hist_line] 322: 877 [M::ha_hist_line] 323: * 870 [M::ha_hist_line] 324: ** 813 [M::ha_hist_line] 325: 774 [M::ha_hist_line] 326: 781 [M::ha_hist_line] 327: 770 [M::ha_hist_line] 328: 767 [M::ha_hist_line] 329: 752 [M::ha_hist_line] 330: 695 [M::ha_hist_line] 331: 737 [M::ha_hist_line] 332: 702 [M::ha_hist_line] 333: 693 [M::ha_hist_line] 334: 683 [M::ha_hist_line] 335: * 653 [M::ha_hist_line] 336: 682 [M::ha_hist_line] 337: 682 [M::ha_hist_line] 338: 642 [M::ha_hist_line] 339: 608 [M::ha_hist_line] 340: 620 [M::ha_hist_line] 341: 616 [M::ha_hist_line] 342: 560 [M::ha_hist_line] 343: 578 [M::ha_hist_line] 344: 541 [M::ha_hist_line] 345: 525 [M::ha_hist_line] 346: 518 [M::ha_hist_line] 347: 593 [M::ha_hist_line] 348: 547 [M::ha_hist_line] 349: 534 [M::ha_hist_line] 350: 527 [M::ha_hist_line] 351: 506 [M::ha_hist_line] 352: 475 [M::ha_hist_line] 353: 470 [M::ha_hist_line] 354: 487 [M::ha_hist_line] 355: 496 [M::ha_hist_line] 356: * 481 [M::ha_hist_line] 357: * 466 [M::ha_hist_line] 358: 496 [M::ha_hist_line] 359: 439 [M::ha_hist_line] 360: 456 [M::ha_hist_line] 361: 448 [M::ha_hist_line] 362: 417 [M::ha_hist_line] 363: 472 [M::ha_hist_line] 364: 435 [M::ha_hist_line] 365: 433 [M::ha_hist_line] 366: 393 [M::ha_hist_line] 367: 402 [M::ha_hist_line] 368: 362 [M::ha_hist_line] 369: 399 [M::ha_hist_line] 370: 381 [M::ha_hist_line] 371: 343 [M::ha_hist_line] 372: 353 [M::ha_hist_line] 373: 372 [M::ha_hist_line] 374: 351 [M::ha_hist_line] 375: 335 [M::ha_hist_line] 376: 346 [M::ha_hist_line] 377: 276 [M::ha_hist_line] 378: 304 [M::ha_hist_line] 379: 308 [M::ha_hist_line] 380: 333 [M::ha_hist_line] 381: 328 [M::ha_hist_line] 382: 276 [M::ha_hist_line] 383: 284 [M::ha_hist_line] 384: 255 [M::ha_hist_line] 385: 272 [M::ha_hist_line] 386: 261 [M::ha_hist_line] 387: 232 [M::ha_hist_line] 388: 258 [M::ha_hist_line] 389: 272 [M::ha_hist_line] 390: 242 [M::ha_hist_line] 391: 242 [M::ha_hist_line] 392: 213 [M::ha_hist_line] 393: 254 [M::ha_hist_line] 394: 244 [M::ha_hist_line] 395: 225 [M::ha_hist_line] 396: 235 [M::ha_hist_line] 397: 228 [M::ha_hist_line] 398: 216 [M::ha_hist_line] 399: 217 [M::ha_hist_line] 400: 200 [M::ha_hist_line] 401: 231 [M::ha_hist_line] 402: 193 [M::ha_hist_line] 403: 199 [M::ha_hist_line] 404: 170 [M::ha_hist_line] 405: 182 [M::ha_hist_line] 406: 198 [M::ha_hist_line] 407: 196 [M::ha_hist_line] 408: 189 [M::ha_hist_line] 409: 189 [M::ha_hist_line] 410: 183 [M::ha_hist_line] 411: 173 [M::ha_hist_line] 412: 158 [M::ha_hist_line] 413: 165 [M::ha_hist_line] 414: 152 [M::ha_hist_line] 415: 165 [M::ha_hist_line] 416: 159 [M::ha_hist_line] 417: 142 [M::ha_hist_line] 418: 167 [M::ha_hist_line] 419: 156 [M::ha_hist_line] 420: 153 [M::ha_hist_line] 421: 141 [M::ha_hist_line] 422: 132 [M::ha_hist_line] 423: 141 [M::ha_hist_line] 424: 147 [M::ha_hist_line] 425: 137 [M::ha_hist_line] 426: 134 [M::ha_hist_line] 427: 151 [M::ha_hist_line] 428: 127 [M::ha_hist_line] 429: 121 [M::ha_hist_line] 430: 118 [M::ha_hist_line] 431: 126 [M::ha_hist_line] 432: 141 [M::ha_hist_line] 433: 122 [M::ha_hist_line] 434: 115 [M::ha_hist_line] 435: 110 [M::ha_hist_line] 436: 119 [M::ha_hist_line] 437: 136 [M::ha_hist_line] 438: 104 [M::ha_hist_line] 439: 98 [M::ha_hist_line] 440: 117 [M::ha_hist_line] 441: 127 [M::ha_hist_line] 442: 109 [M::ha_hist_line] rest: ***** 6401 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 106; peak_het: -1 [M::ha_pt_gen::10033.11111.32] ==> indexed 434636756 positions [M::ha_assemble::12996.87011.47@19.708GB] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 2729153 [M::ha_print_ovlp_stat] # strong overlaps: 27392 [M::ha_print_ovlp_stat] # weak overlaps: 2701761 [M::ha_print_ovlp_stat] # exact overlaps: 1918623 [M::ha_print_ovlp_stat] # inexact overlaps: 810530 [M::ha_print_ovlp_stat] # overlaps without large indels: 2722140 [M::ha_print_ovlp_stat] # reverse overlaps: 26443 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: 10 [M::mc_solve:: # edges: 0] [M::mc_solve_core::0.000] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [6, infinity] Writing VX0223.asm.run7.bp.p_ctg.gfa to disk... Writing VX0223.asm.run7.bp.hap1.p_ctg.gfa to disk... [M::adjust_utg_by_trio] primary contig coverage range: [6, infinity] Writing VX0223.asm.run7.bp.hap2.p_ctg.gfa to disk... [M::adjust_utg_by_trio] primary contig coverage range: [6, infinity] Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.15.1-r334 [M::main] CMD: /projects/phillipslab/ateterina/scripts/hifiasm/hifiasm -o VX0223.asm.run7 -t24 --purge-cov 10 /projects/phillipslab/ateterina/Cbren/assembly/HIFI/willis_ccs.subreads.fastq.gz [M::main] Real time: 13009.830 sec; CPU: 149105.390 sec; Peak RSS: 19.708 GB

attrna commented 3 years ago

Also, this is an inbred strain, so it shouldn't have much variation. The final stats were pretty much the same for the different parameters I tried.

chhylp123 commented 3 years ago

The problem is the data. The k-mer plot of good hifi data should be: https://github.com/chhylp123/hifiasm/issues/49#issue-729106823. Looks like there are something wrong for the hifi reads.

attrna commented 3 years ago

Thank you for your reply! Probably, this is due to the individual-worm amplification, many of the regions are overrepresented... How do you think is it possible to do something in this case? Maybe I should change the k-mer size or the coverage threshold? Or maybe prefilter the data somehow?

chhylp123 commented 3 years ago

Sorry I have no idea either.. usually hifiasm cannot get good results in this case.

jelber2 commented 3 years ago

You could prefilter the data with dedupe.sh from BBTools. Not sure of recommendations for settings. You could also try simulating WGA reads with randomreads.sh from BBTools as well if I remember correctly to try and get an idea of dedupe.sh settings.

Update: you might give BBNorm a try as well.

attrna commented 3 years ago

Thank you!! I'll try it.

scottgeib commented 3 years ago

did you run the hifi data through pcr dup removal using pbmarkdup as part of their ultralow input protocol? https://github.com/PacificBiosciences/pbmarkdup/