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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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discontinuous assembly with shorter pacbio hifi reads but high coverage #639

Open leqi0001 opened 7 months ago

leqi0001 commented 7 months ago

Hi,

Thanks for developing the package!

I have a few dozens of samples with captured PacBio hifi reads averaging 4kb in length but >200x coverage in a 1.6Mb human genome region, which has a lot of high frequency CNVs and other rearrangements. My testing with hifiasm gave me on average 500kb longest primary contigs, with a bunch of small contigs. I tried to --hg-size 1.6M, increased -D and -N and all of these helped to increase the length to 800Kb or so. Would you have suggestions for further improving the length of the assembly? I know previous post suggested that higher coverage might hurt sometimes. Is there a way to downsample the reads to get lower but a more even coverage of the region?

chhylp123 commented 7 months ago

Sorry for the late reply. Could you please show the log file?

leqi0001 commented 7 months ago

No worries! I've tried down-sampling the reads so that there's a maximum coverage cutoff of 50x in the whole region of interests. The results are almost identical as before.

Here's an example log file:

Loading R/4.3.0 Loading requirement: intel/2022.1.1 java/jdk-11.0.14 [M::ha_analyze_count] lowest: count[8] = 5120 [M::ha_analyze_count] highest: count[41] = 8241 [M::ha_hist_line] 2: ****> 95517 [M::ha_hist_line] 3: ****> 16614 [M::ha_hist_line] 4: ****> 11034 [M::ha_hist_line] 5: ****> 8524 [M::ha_hist_line] 6: ***** 7694 [M::ha_hist_line] 7: **** 7579 [M::ha_hist_line] 8: ** 5120 [M::ha_hist_line] 9: ** 6097 [M::ha_hist_line] 10: **** 5247 [M::ha_hist_line] 11: * 4402 [M::ha_hist_line] 12: *** 4839 [M::ha_hist_line] 13: ** 4452 [M::ha_hist_line] 14: * 4053 [M::ha_hist_line] 15: ** 4446 [M::ha_hist_line] 16: **** 4982 [M::ha_hist_line] 17: *** 4705 [M::ha_hist_line] 18: ** 4785 [M::ha_hist_line] 19: ** 3781 [M::ha_hist_line] 20: ** 4116 [M::ha_hist_line] 21: * 3836 [M::ha_hist_line] 22: *** 3670 [M::ha_hist_line] 23: ** 3761 [M::ha_hist_line] 24: **** 3960 [M::ha_hist_line] 25: **** 3271 [M::ha_hist_line] 26: **** 3647 [M::ha_hist_line] 27: * 2585 [M::ha_hist_line] 28: ** 2510 [M::ha_hist_line] 29: * 3237 [M::ha_hist_line] 30: **** 2983 [M::ha_hist_line] 31: ** 3440 [M::ha_hist_line] 32: *** 3713 [M::ha_hist_line] 33: * 4182 [M::ha_hist_line] 34: **** 5565 [M::ha_hist_line] 35: ***** 5160 [M::ha_hist_line] 36: * 4837 [M::ha_hist_line] 37: *** 5320 [M::ha_hist_line] 38: ** 5739 [M::ha_hist_line] 39: **** 6242 [M::ha_hist_line] 40: *** 7312 [M::ha_hist_line] 41: **** 8241 [M::ha_hist_line] 42: ** 7383 [M::ha_hist_line] 43: **** 6245 [M::ha_hist_line] 44: ** 6061 [M::ha_hist_line] 45: * 6213 [M::ha_hist_line] 46: ***** 6183 [M::ha_hist_line] 47: **** 5587 [M::ha_hist_line] 48: * 5151 [M::ha_hist_line] 49: ***** 5223 [M::ha_hist_line] 50: ** 5419 [M::ha_hist_line] 51: * 4547 [M::ha_hist_line] 52: **** 5234 [M::ha_hist_line] 53: * 5230 [M::ha_hist_line] 54: ***** 5540 [M::ha_hist_line] 55: 4893 [M::ha_hist_line] 56: 4882 [M::ha_hist_line] 57: * 5033 [M::ha_hist_line] 58: **** 4915 [M::ha_hist_line] 59: ***** 5708 [M::ha_hist_line] 60: ** 5145 [M::ha_hist_line] 61: ** 4757 [M::ha_hist_line] 62: ** 5448 [M::ha_hist_line] 63: ** 5136 [M::ha_hist_line] 64: * 4881 [M::ha_hist_line] 65: ** 5135 [M::ha_hist_line] 66: ***** 5511 [M::ha_hist_line] 67: ** 6401 [M::ha_hist_line] 68: **** 5922 [M::ha_hist_line] 69: ** 6404 [M::ha_hist_line] 70: * 5866 [M::ha_hist_line] 71: *** 6379 [M::ha_hist_line] 72: **** 6285 [M::ha_hist_line] 73: **** 5862 [M::ha_hist_line] 74: 5500 [M::ha_hist_line] 75: ** 5131 [M::ha_hist_line] 76: ** 5141 [M::ha_hist_line] 77: * 5346 [M::ha_hist_line] 78: ***** 6028 [M::ha_hist_line] 79: **** 5912 [M::ha_hist_line] 80: * 5889 [M::ha_hist_line] 81: *** 6713 [M::ha_hist_line] 82: * 6025 [M::ha_hist_line] 83: *** 6140 [M::ha_hist_line] 84: **** 5293 [M::ha_hist_line] 85: ** 6440 [M::ha_hist_line] 86: **** 6242 [M::ha_hist_line] 87: ***** 5874 [M::ha_hist_line] 88: **** 4961 [M::ha_hist_line] 89: * 4903 [M::ha_hist_line] 90: * 4680 [M::ha_hist_line] 91: **** 4583 [M::ha_hist_line] 92: ** 4784 [M::ha_hist_line] 93: ** 5448 [M::ha_hist_line] 94: ***** 6037 [M::ha_hist_line] 95: *** 6473 [M::ha_hist_line] 96: **** 5252 [M::ha_hist_line] 97: * 5359 [M::ha_hist_line] 98: **** 5251 [M::ha_hist_line] 99: **** 6271 [M::ha_hist_line] 100: ** 6220 [M::ha_hist_line] 101: 6037 [M::ha_hist_line] 102: ** 5144 [M::ha_hist_line] 103: * 5485 [M::ha_hist_line] 104: **** 5587 [M::ha_hist_line] 105: **** 5257 [M::ha_hist_line] 106: ** 5459 [M::ha_hist_line] 107: **** 5577 [M::ha_hist_line] 108: ** 5784 [M::ha_hist_line] 109: ***** 5815 [M::ha_hist_line] 110: ** 6357 [M::ha_hist_line] 111: 6156 [M::ha_hist_line] 112: ** 6862 [M::ha_hist_line] 113: 6664 [M::ha_hist_line] 114: **** 6331 [M::ha_hist_line] 115: 6012 [M::ha_hist_line] 116: ** 5753 [M::ha_hist_line] 117: **** 5870 [M::ha_hist_line] 118: 5490 [M::ha_hist_line] 119: ** 5112 [M::ha_hist_line] 120: ** 4887 [M::ha_hist_line] 121: 4699 [M::ha_hist_line] 122: **** 4318 [M::ha_hist_line] 123: ** 4449 [M::ha_hist_line] 124: ** 4151 [M::ha_hist_line] 125: **** 4322 [M::ha_hist_line] 126: * 4188 [M::ha_hist_line] 127: **** 3918 [M::ha_hist_line] 128: * 4208 [M::ha_hist_line] 129: ** 4116 [M::ha_hist_line] 130: **** 3872 [M::ha_hist_line] 131: 3539 [M::ha_hist_line] 132: **** 3341 [M::ha_hist_line] 133: 3077 [M::ha_hist_line] 134: **** 2666 [M::ha_hist_line] 135: * 3078 [M::ha_hist_line] 136: *** 3207 [M::ha_hist_line] 137: ** 2792 [M::ha_hist_line] 138: * 2537 [M::ha_hist_line] 139: *** 3047 [M::ha_hist_line] 140: **** 2317 [M::ha_hist_line] 141: *** 2551 [M::ha_hist_line] 142: * 2096 [M::ha_hist_line] 143: *** 1931 [M::ha_hist_line] 144: **** 1946 [M::ha_hist_line] 145: **** 1969 [M::ha_hist_line] 146: ** 1805 [M::ha_hist_line] 147: ** 1453 [M::ha_hist_line] 148: * 1420 [M::ha_hist_line] 149: * 1407 [M::ha_hist_line] 150: **** 1304 [M::ha_hist_line] 151: * 1392 [M::ha_hist_line] 152: **** 1303 [M::ha_hist_line] 153: * 1394 [M::ha_hist_line] 154: ** 1297 [M::ha_hist_line] 155: * 1248 [M::ha_hist_line] 156: **** 948 [M::ha_hist_line] 157: * 1109 [M::ha_hist_line] 158: **** 865 [M::ha_hist_line] 159: **** 1004 [M::ha_hist_line] 160: * 927 [M::ha_hist_line] 161: ** 1154 [M::ha_hist_line] 162: 1054 [M::ha_hist_line] 163: 1109 [M::ha_hist_line] 164: * 1076 [M::ha_hist_line] 165: ** 1137 [M::ha_hist_line] 166: ** 1190 [M::ha_hist_line] 167: ** 1167 [M::ha_hist_line] 168: * 1057 [M::ha_hist_line] 169: ** 1095 [M::ha_hist_line] 170: 875 [M::ha_hist_line] 171: **** 969 [M::ha_hist_line] 172: **** 1010 [M::ha_hist_line] 173: **** 951 [M::ha_hist_line] 174: * 1248 [M::ha_hist_line] 175: ** 1300 [M::ha_hist_line] 176: ** 1128 [M::ha_hist_line] 177: **** 969 [M::ha_hist_line] 178: ** 1163 [M::ha_hist_line] 179: ** 1155 [M::ha_hist_line] 180: **** 1015 [M::ha_hist_line] 181: * 1097 [M::ha_hist_line] 182: 1052 [M::ha_hist_line] 183: 1095 [M::ha_hist_line] 184: **** 1015 [M::ha_hist_line] 185: ** 1132 [M::ha_hist_line] 186: **** 1003 [M::ha_hist_line] 187: * 760 [M::ha_hist_line] 188: ** 697 [M::ha_hist_line] 189: * 598 [M::ha_hist_line] 190: * 715 [M::ha_hist_line] 191: **** 669 [M::ha_hist_line] 192: **** 624 [M::ha_hist_line] 193: * 711 [M::ha_hist_line] 194: 447 [M::ha_hist_line] 195: 402 [M::ha_hist_line] 196: * 559 [M::ha_hist_line] 197: **** 461 [M::ha_hist_line] 198: ** 463 [M::ha_hist_line] 199: 303 [M::ha_hist_line] 200: 320 [M::ha_hist_line] 201: * 377 [M::ha_hist_line] 202: * 409 [M::ha_hist_line] 203: **** 465 [M::ha_hist_line] 204: 325 [M::ha_hist_line] 205: 297 [M::ha_hist_line] 206: * 249 [M::ha_hist_line] 207: ** 299 [M::ha_hist_line] 208: ** 255 [M::ha_hist_line] 209: 232 [M::ha_hist_line] 210: * 247 [M::ha_hist_line] 211: * 197 [M::ha_hist_line] 212: 288 [M::ha_hist_line] 213: 335 [M::ha_hist_line] 214: 308 [M::ha_hist_line] 215: 232 [M::ha_hist_line] 216: 282 [M::ha_hist_line] 217: ** 383 [M::ha_hist_line] 218: 267 [M::ha_hist_line] 219: * 263 [M::ha_hist_line] 220: *** 305 [M::ha_hist_line] 221: 277 [M::ha_hist_line] 222: 255 [M::ha_hist_line] 223: 259 [M::ha_hist_line] 224: 232 [M::ha_hist_line] 225: 204 [M::ha_hist_line] 226: 180 [M::ha_hist_line] 227: 269 [M::ha_hist_line] 228: 180 [M::ha_hist_line] 229: 216 [M::ha_hist_line] 230: 204 [M::ha_hist_line] 231: 211 [M::ha_hist_line] 232: 195 [M::ha_hist_line] 233: * 265 [M::ha_hist_line] 234: ** 324 [M::ha_hist_line] 235: 296 [M::ha_hist_line] 236: 318 [M::ha_hist_line] 237: *** 365 [M::ha_hist_line] 238: 243 [M::ha_hist_line] 239: 227 [M::ha_hist_line] 240: 220 [M::ha_hist_line] 241: * 228 [M::ha_hist_line] 242: 148 [M::ha_hist_line] 243: 182 [M::ha_hist_line] 244: 158 [M::ha_hist_line] 245: 144 [M::ha_hist_line] 246: * 128 [M::ha_hist_line] 247: 73 [M::ha_hist_line] 248: 81 [M::ha_hist_line] 249: 50 [M::ha_hist_line] 250: 64 [M::ha_hist_line] 251: 50 [M::ha_hist_line] 252: 56 [M::ha_hist_line] 253: 67 [M::ha_hist_line] rest: **> 10248 [M::ha_analyze_count] left: count[9] = 6097 [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 41; peak_het: 9 [M::ha_ct_shrink::15.1681.67] ==> counted 2 distinct minimizer k-mers [M::ha_ft_gen::15.1881.67@16.483GB] ==> filtered out 2 k-mers occurring 4094 or more times [M::ha_opt_update_cov] updated max_n_chain to 41000 [M::yak_count] collected 2671532 minimizers [M::ha_pt_gen::16.414*1.87] ==> counted 91858 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[8] = 211 [M::ha_analyze_count] highest: count[41] = 319 [M::ha_hist_line] 1: ****> 54741 [M::ha_hist_line] 2: ****> 5040 [M::ha_hist_line] 3: ****> 1024 [M::ha_hist_line] 4: ****> 544 [M::ha_hist_line] 5: ****> 382 [M::ha_hist_line] 6: **** 308 [M::ha_hist_line] 7: 298 [M::ha_hist_line] 8: ** 211 [M::ha_hist_line] 9: *** 246 [M::ha_hist_line] 10: ** 210 [M::ha_hist_line] 11: * 187 [M::ha_hist_line] 12: ** 185 [M::ha_hist_line] 13: * 174 [M::ha_hist_line] 14: ** 146 [M::ha_hist_line] 15: ** 173 [M::ha_hist_line] 16: ***** 202 [M::ha_hist_line] 17: ** 198 [M::ha_hist_line] 18: *** 182 [M::ha_hist_line] 19: * 162 [M::ha_hist_line] 20: * 169 [M::ha_hist_line] 21: **** 148 [M::ha_hist_line] 22: * 163 [M::ha_hist_line] 23: 150 [M::ha_hist_line] 24: 150 [M::ha_hist_line] 25: ***** 137 [M::ha_hist_line] 26: **** 140 [M::ha_hist_line] 27: * 100 [M::ha_hist_line] 28: 118 [M::ha_hist_line] 29: 118 [M::ha_hist_line] 30: **** 140 [M::ha_hist_line] 31: **** 140 [M::ha_hist_line] 32: * 157 [M::ha_hist_line] 33: *** 175 [M::ha_hist_line] 34: ***** 232 [M::ha_hist_line] 35: * 196 [M::ha_hist_line] 36: ** 186 [M::ha_hist_line] 37: * 201 [M::ha_hist_line] 38: **** 230 [M::ha_hist_line] 39: ***** 264 [M::ha_hist_line] 40: ***** 310 [M::ha_hist_line] 41: **** 319 [M::ha_hist_line] 42: ** 286 [M::ha_hist_line] 43: * 207 [M::ha_hist_line] 44: **** 256 [M::ha_hist_line] 45: ***** 233 [M::ha_hist_line] 46: ** 223 [M::ha_hist_line] 47: ** 248 [M::ha_hist_line] 48: * 207 [M::ha_hist_line] 49: **** 216 [M::ha_hist_line] 50: * 206 [M::ha_hist_line] 51: **** 179 [M::ha_hist_line] 52: *** 227 [M::ha_hist_line] 53: ** 186 [M::ha_hist_line] 54: * 194 [M::ha_hist_line] 55: ***** 234 [M::ha_hist_line] 56: **** 190 [M::ha_hist_line] 57: * 201 [M::ha_hist_line] 58: ***** 214 [M::ha_hist_line] 59: ***** 220 [M::ha_hist_line] 60: * 195 [M::ha_hist_line] 61: **** 203 [M::ha_hist_line] 62: ** 197 [M::ha_hist_line] 63: ** 199 [M::ha_hist_line] 64: **** 206 [M::ha_hist_line] 65: 195 [M::ha_hist_line] 66: **** 230 [M::ha_hist_line] 67: **** 267 [M::ha_hist_line] 68: **** 242 [M::ha_hist_line] 69: **** 244 [M::ha_hist_line] 70: * 240 [M::ha_hist_line] 71: ** 237 [M::ha_hist_line] 72: ** 223 [M::ha_hist_line] 73: * 240 [M::ha_hist_line] 74: **** 216 [M::ha_hist_line] 75: **** 190 [M::ha_hist_line] 76: ** 210 [M::ha_hist_line] 77: ** 199 [M::ha_hist_line] 78: * 232 [M::ha_hist_line] 79: ** 235 [M::ha_hist_line] 80: * 232 [M::ha_hist_line] 81: ***** 278 [M::ha_hist_line] 82: * 228 [M::ha_hist_line] 83: * 233 [M::ha_hist_line] 84: *** 238 [M::ha_hist_line] 85: **** 230 [M::ha_hist_line] 86: ** 222 [M::ha_hist_line] 87: ** 210 [M::ha_hist_line] 88: * 187 [M::ha_hist_line] 89: ** 192 [M::ha_hist_line] 90: * 182 [M::ha_hist_line] 91: * 163 [M::ha_hist_line] 92: *** 219 [M::ha_hist_line] 93: 225 [M::ha_hist_line] 94: 228 [M::ha_hist_line] 95: *** 247 [M::ha_hist_line] 96: * 215 [M::ha_hist_line] 97: * 208 [M::ha_hist_line] 98: **** 204 [M::ha_hist_line] 99: ** 249 [M::ha_hist_line] 100: *** 226 [M::ha_hist_line] 101: * 213 [M::ha_hist_line] 102: ***** 225 [M::ha_hist_line] 103: * 189 [M::ha_hist_line] 104: ***** 215 [M::ha_hist_line] 105: * 225 [M::ha_hist_line] 106: **** 229 [M::ha_hist_line] 107: * 215 [M::ha_hist_line] 108: *** 258 [M::ha_hist_line] 109: * 226 [M::ha_hist_line] 110: **** 243 [M::ha_hist_line] 111: ** 224 [M::ha_hist_line] 112: **** 268 [M::ha_hist_line] 113: ***** 266 [M::ha_hist_line] 114: ** 224 [M::ha_hist_line] 115: ** 209 [M::ha_hist_line] 116: **** 229 [M::ha_hist_line] 117: * 227 [M::ha_hist_line] 118: 196 [M::ha_hist_line] 119: 194 [M::ha_hist_line] 120: * 181 [M::ha_hist_line] 121: **** 171 [M::ha_hist_line] 122: ** 184 [M::ha_hist_line] 123: ** 171 [M::ha_hist_line] 124: * 176 [M::ha_hist_line] 125: ** 159 [M::ha_hist_line] 126: *** 175 [M::ha_hist_line] 127: **** 128 [M::ha_hist_line] 128: * 156 [M::ha_hist_line] 129: *** 132 [M::ha_hist_line] 130: **** 153 [M::ha_hist_line] 131: * 112 [M::ha_hist_line] 132: * 125 [M::ha_hist_line] 133: **** 116 [M::ha_hist_line] 134: ** 108 [M::ha_hist_line] 135: ** 96 [M::ha_hist_line] 136: * 126 [M::ha_hist_line] 137: ** 109 [M::ha_hist_line] 138: *** 118 [M::ha_hist_line] 139: ** 109 [M::ha_hist_line] 140: ** 83 [M::ha_hist_line] 141: * 86 [M::ha_hist_line] 142: ** 70 [M::ha_hist_line] 143: 72 [M::ha_hist_line] 144: 72 [M::ha_hist_line] 145: ** 71 [M::ha_hist_line] 146: * 55 [M::ha_hist_line] 147: **** 50 [M::ha_hist_line] 148: ** 45 [M::ha_hist_line] 149: ** 46 [M::ha_hist_line] 150: *** 61 [M::ha_hist_line] 151: ** 46 [M::ha_hist_line] 152: **** 51 [M::ha_hist_line] 153: **** 51 [M::ha_hist_line] 154: 41 [M::ha_hist_line] 155: 43 [M::ha_hist_line] 156: * 35 [M::ha_hist_line] 157: **** 38 [M::ha_hist_line] 158: ** 31 [M::ha_hist_line] 159: ** 32 [M::ha_hist_line] 160: ** 45 [M::ha_hist_line] 161: ** 45 [M::ha_hist_line] 162: *** 43 [M::ha_hist_line] 163: **** 37 [M::ha_hist_line] 164: ** 40 [M::ha_hist_line] 165: 36 [M::ha_hist_line] 166: **** 50 [M::ha_hist_line] 167: ** 45 [M::ha_hist_line] 168: * 36 [M::ha_hist_line] 169: ** 46 [M::ha_hist_line] 170: **** 52 [M::ha_hist_line] 171: * 36 [M::ha_hist_line] 172: ** 33 [M::ha_hist_line] 173: *** 47 [M::ha_hist_line] 174: **** 50 [M::ha_hist_line] 175: **** 51 [M::ha_hist_line] 176: ** 45 [M::ha_hist_line] 177: **** 38 [M::ha_hist_line] 178: * 28 [M::ha_hist_line] 179: ** 45 [M::ha_hist_line] 180: * 40 [M::ha_hist_line] 181: ** 45 [M::ha_hist_line] 182: **** 39 [M::ha_hist_line] 183: ** 33 [M::ha_hist_line] 184: * 41 [M::ha_hist_line] 185: * 40 [M::ha_hist_line] 186: **** 37 [M::ha_hist_line] 187: ** 31 [M::ha_hist_line] 188: ** 19 [M::ha_hist_line] 189: * 30 [M::ha_hist_line] 190: * 23 [M::ha_hist_line] 191: **** 25 [M::ha_hist_line] 192: * 23 [M::ha_hist_line] 193: ** 23 [M::ha_hist_line] 194: 16 [M::ha_hist_line] 195: ** 14 [M::ha_hist_line] 196: *** 21 [M::ha_hist_line] 197: ** 20 [M::ha_hist_line] 198: * 10 [M::ha_hist_line] 199: * 17 [M::ha_hist_line] 200: ** 12 [M::ha_hist_line] 201: ** 20 [M::ha_hist_line] 202: 12 [M::ha_hist_line] 203: 13 [M::ha_hist_line] 204: * 10 [M::ha_hist_line] 205: 10 [M::ha_hist_line] 206: 5 [M::ha_hist_line] 207: 16 [M::ha_hist_line] 208: 9 [M::ha_hist_line] 209: 3 [M::ha_hist_line] 210: ** 12 [M::ha_hist_line] 211: ** 12 [M::ha_hist_line] 212: ** 11 [M::ha_hist_line] 213: 9 [M::ha_hist_line] 214: 9 [M::ha_hist_line] 215: 9 [M::ha_hist_line] 216: ** 12 [M::ha_hist_line] 217: * 9 [M::ha_hist_line] 218: ** 14 [M::ha_hist_line] 219: * 3 [M::ha_hist_line] 220: ** 9 [M::ha_hist_line] 221: 9 [M::ha_hist_line] 222: 6 [M::ha_hist_line] 223: 6 [M::ha_hist_line] 224: 7 [M::ha_hist_line] 225: ** 9 [M::ha_hist_line] 226: 10 [M::ha_hist_line] 227: 11 [M::ha_hist_line] 228: 2 [M::ha_hist_line] 229: ** 9 [M::ha_hist_line] 230: 10 [M::ha_hist_line] 231: 7 [M::ha_hist_line] 232: 6 [M::ha_hist_line] 233: ** 12 [M::ha_hist_line] 234: * 9 [M::ha_hist_line] 235: ** 13 [M::ha_hist_line] 236: *** 13 [M::ha_hist_line] 237: 9 [M::ha_hist_line] 238: 6 [M::ha_hist_line] 239: 5 [M::ha_hist_line] 240: * 8 [M::ha_hist_line] 241: * 6 [M::ha_hist_line] 242: 3 [M::ha_hist_line] 243: 7 [M::ha_hist_line] 244: 6 [M::ha_hist_line] 245: 5 [M::ha_hist_line] 246: 3 [M::ha_hist_line] 247: 2 [M::ha_hist_line] 248: * 2 [M::ha_hist_line] rest: ****> 385 [M::ha_analyze_count] left: count[9] = 246 [M::ha_analyze_count] right: count[81] = 278 [M::ha_pt_gen] peak_hom: 41; peak_het: 9 [M::ha_ct_shrink::16.4341.87] ==> counted 37117 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2671532 minimizers [M::ha_pt_gen::16.9602.09] ==> indexed 2616791 positions, counted 37117 distinct minimizer k-mers [M::ha_assemble::41.42312.88@16.483GB] ==> corrected reads for round 1 [M::ha_assemble] # bases: 100589746; # corrected bases: 127238; # recorrected bases: 725 [M::ha_assemble] size of buffer: 0.700GB [M::yak_count] collected 2671240 minimizers [M::ha_pt_gen::41.89712.84] ==> counted 36621 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 254 [M::ha_analyze_count] highest: count[42] = 343 [M::ha_hist_line] 1: ****> 4261 [M::ha_hist_line] 2: ****> 1115 [M::ha_hist_line] 3: ****> 555 [M::ha_hist_line] 4: ****> 368 [M::ha_hist_line] 5: **** 316 [M::ha_hist_line] 6: ** 254 [M::ha_hist_line] 7: **** 289 [M::ha_hist_line] 8: * 187 [M::ha_hist_line] 9: *** 222 [M::ha_hist_line] 10: *** 208 [M::ha_hist_line] 11: ** 172 [M::ha_hist_line] 12: * 174 [M::ha_hist_line] 13: * 181 [M::ha_hist_line] 14: ** 158 [M::ha_hist_line] 15: ** 143 [M::ha_hist_line] 16: *** 189 [M::ha_hist_line] 17: ** 170 [M::ha_hist_line] 18: *** 216 [M::ha_hist_line] 19: * 128 [M::ha_hist_line] 20: ***** 175 [M::ha_hist_line] 21: ** 158 [M::ha_hist_line] 22: * 149 [M::ha_hist_line] 23: * 128 [M::ha_hist_line] 24: **** 170 [M::ha_hist_line] 25: **** 138 [M::ha_hist_line] 26: ** 143 [M::ha_hist_line] 27: ** 102 [M::ha_hist_line] 28: **** 111 [M::ha_hist_line] 29: ** 116 [M::ha_hist_line] 30: * 121 [M::ha_hist_line] 31: * 121 [M::ha_hist_line] 32: **** 123 [M::ha_hist_line] 33: **** 166 [M::ha_hist_line] 34: **** 207 [M::ha_hist_line] 35: *** 210 [M::ha_hist_line] 36: ** 159 [M::ha_hist_line] 37: ** 185 [M::ha_hist_line] 38: *** 244 [M::ha_hist_line] 39: * 167 [M::ha_hist_line] 40: **** 274 [M::ha_hist_line] 41: ***** 338 [M::ha_hist_line] 42: **** 343 [M::ha_hist_line] 43: ** 253 [M::ha_hist_line] 44: ** 225 [M::ha_hist_line] 45: ** 239 [M::ha_hist_line] 46: ** 228 [M::ha_hist_line] 47: **** 207 [M::ha_hist_line] 48: ** 239 [M::ha_hist_line] 49: ** 211 [M::ha_hist_line] 50: **** 207 [M::ha_hist_line] 51: * 201 [M::ha_hist_line] 52: ***** 209 [M::ha_hist_line] 53: **** 207 [M::ha_hist_line] 54: ** 184 [M::ha_hist_line] 55: * 183 [M::ha_hist_line] 56: **** 163 [M::ha_hist_line] 57: *** 217 [M::ha_hist_line] 58: **** 177 [M::ha_hist_line] 59: ** 240 [M::ha_hist_line] 60: * 196 [M::ha_hist_line] 61: * 183 [M::ha_hist_line] 62: **** 192 [M::ha_hist_line] 63: ** 185 [M::ha_hist_line] 64: * 183 [M::ha_hist_line] 65: * 197 [M::ha_hist_line] 66: **** 206 [M::ha_hist_line] 67: **** 233 [M::ha_hist_line] 68: ** 240 [M::ha_hist_line] 69: ** 253 [M::ha_hist_line] 70: *** 245 [M::ha_hist_line] 71: ** 250 [M::ha_hist_line] 72: 244 [M::ha_hist_line] 73: ** 223 [M::ha_hist_line] 74: 215 [M::ha_hist_line] 75: **** 205 [M::ha_hist_line] 76: **** 218 [M::ha_hist_line] 77: *** 215 [M::ha_hist_line] 78: * 183 [M::ha_hist_line] 79: * 201 [M::ha_hist_line] 80: ** 200 [M::ha_hist_line] 81: ***** 256 [M::ha_hist_line] 82: **** 273 [M::ha_hist_line] 83: * 217 [M::ha_hist_line] 84: ** 226 [M::ha_hist_line] 85: **** 232 [M::ha_hist_line] 86: * 215 [M::ha_hist_line] 87: **** 247 [M::ha_hist_line] 88: ** 226 [M::ha_hist_line] 89: ** 170 [M::ha_hist_line] 90: *** 188 [M::ha_hist_line] 91: * 153 [M::ha_hist_line] 92: ** 184 [M::ha_hist_line] 93: **** 205 [M::ha_hist_line] 94: * 216 [M::ha_hist_line] 95: **** 259 [M::ha_hist_line] 96: ** 213 [M::ha_hist_line] 97: ** 157 [M::ha_hist_line] 98: *** 224 [M::ha_hist_line] 99: *** 235 [M::ha_hist_line] 100: ** 241 [M::ha_hist_line] 101: **** 218 [M::ha_hist_line] 102: * 216 [M::ha_hist_line] 103: * 208 [M::ha_hist_line] 104: ** 185 [M::ha_hist_line] 105: * 208 [M::ha_hist_line] 106: * 188 [M::ha_hist_line] 107: **** 221 [M::ha_hist_line] 108: ** 239 [M::ha_hist_line] 109: **** 220 [M::ha_hist_line] 110: ** 199 [M::ha_hist_line] 111: **** 193 [M::ha_hist_line] 112: *** 251 [M::ha_hist_line] 113: **** 301 [M::ha_hist_line] 114: 252 [M::ha_hist_line] 115: 251 [M::ha_hist_line] 116: ** 226 [M::ha_hist_line] 117: 209 [M::ha_hist_line] 118: 209 [M::ha_hist_line] 119: ** 213 [M::ha_hist_line] 120: *** 224 [M::ha_hist_line] 121: ** 184 [M::ha_hist_line] 122: **** 179 [M::ha_hist_line] 123: * 175 [M::ha_hist_line] 124: *** 181 [M::ha_hist_line] 125: ** 170 [M::ha_hist_line] 126: **** 166 [M::ha_hist_line] 127: * 147 [M::ha_hist_line] 128: **** 150 [M::ha_hist_line] 129: * 154 [M::ha_hist_line] 130: ***** 169 [M::ha_hist_line] 131: * 155 [M::ha_hist_line] 132: *** 161 [M::ha_hist_line] 133: ** 130 [M::ha_hist_line] 134: * 127 [M::ha_hist_line] 135: ** 118 [M::ha_hist_line] 136: * 114 [M::ha_hist_line] 137: * 113 [M::ha_hist_line] 138: ** 110 [M::ha_hist_line] 139: * 107 [M::ha_hist_line] 140: ** 115 [M::ha_hist_line] 141: ** 104 [M::ha_hist_line] 142: **** 96 [M::ha_hist_line] 143: ** 88 [M::ha_hist_line] 144: * 72 [M::ha_hist_line] 145: *** 78 [M::ha_hist_line] 146: **** 56 [M::ha_hist_line] 147: *** 73 [M::ha_hist_line] 148: ** 61 [M::ha_hist_line] 149: ** 76 [M::ha_hist_line] 150: * 51 [M::ha_hist_line] 151: 43 [M::ha_hist_line] 152: 45 [M::ha_hist_line] 153: * 51 [M::ha_hist_line] 154: ** 62 [M::ha_hist_line] 155: **** 55 [M::ha_hist_line] 156: ** 61 [M::ha_hist_line] 157: ** 48 [M::ha_hist_line] 158: ** 33 [M::ha_hist_line] 159: **** 40 [M::ha_hist_line] 160: ** 36 [M::ha_hist_line] 161: ** 34 [M::ha_hist_line] 162: ** 36 [M::ha_hist_line] 163: * 39 [M::ha_hist_line] 164: * 37 [M::ha_hist_line] 165: *** 46 [M::ha_hist_line] 166: ** 35 [M::ha_hist_line] 167: * 31 [M::ha_hist_line] 168: *** 50 [M::ha_hist_line] 169: ** 49 [M::ha_hist_line] 170: ** 34 [M::ha_hist_line] 171: **** 26 [M::ha_hist_line] 172: ** 49 [M::ha_hist_line] 173: **** 41 [M::ha_hist_line] 174: ** 49 [M::ha_hist_line] 175: **** 55 [M::ha_hist_line] 176: ** 33 [M::ha_hist_line] 177: ** 48 [M::ha_hist_line] 178: **** 40 [M::ha_hist_line] 179: ** 34 [M::ha_hist_line] 180: * 30 [M::ha_hist_line] 181: ** 47 [M::ha_hist_line] 182: *** 50 [M::ha_hist_line] 183: * 32 [M::ha_hist_line] 184: *** 39 [M::ha_hist_line] 185: * 32 [M::ha_hist_line] 186: ** 47 [M::ha_hist_line] 187: *** 50 [M::ha_hist_line] 188: ***** 44 [M::ha_hist_line] 189: ** 33 [M::ha_hist_line] 190: **** 40 [M::ha_hist_line] 191: * 16 [M::ha_hist_line] 192: **** 27 [M::ha_hist_line] 193: * 24 [M::ha_hist_line] 194: ** 34 [M::ha_hist_line] 195: *** 30 [M::ha_hist_line] 196: * 32 [M::ha_hist_line] 197: ** 19 [M::ha_hist_line] 198: * 17 [M::ha_hist_line] 199: 12 [M::ha_hist_line] 200: 12 [M::ha_hist_line] 201: * 5 [M::ha_hist_line] 202: * 12 [M::ha_hist_line] 203: 13 [M::ha_hist_line] 204: 15 [M::ha_hist_line] 205: * 11 [M::ha_hist_line] 206: * 12 [M::ha_hist_line] 207: ***** 25 [M::ha_hist_line] 208: * 10 [M::ha_hist_line] 209: 8 [M::ha_hist_line] 210: ** 13 [M::ha_hist_line] 211: * 11 [M::ha_hist_line] 212: 7 [M::ha_hist_line] 213: ** 14 [M::ha_hist_line] 214: * 11 [M::ha_hist_line] 215: *** 13 [M::ha_hist_line] 216: 10 [M::ha_hist_line] 217: 5 [M::ha_hist_line] 218: 4 [M::ha_hist_line] 219: ** 18 [M::ha_hist_line] 220: 12 [M::ha_hist_line] 221: * 11 [M::ha_hist_line] 222: ** 15 [M::ha_hist_line] 223: 8 [M::ha_hist_line] 224: 8 [M::ha_hist_line] 225: 5 [M::ha_hist_line] 226: 5 [M::ha_hist_line] 227: 3 [M::ha_hist_line] 228: 9 [M::ha_hist_line] 229: * 7 [M::ha_hist_line] 230: 5 [M::ha_hist_line] 231: 7 [M::ha_hist_line] 232: 7 [M::ha_hist_line] 233: * 10 [M::ha_hist_line] 234: 6 [M::ha_hist_line] 235: * 6 [M::ha_hist_line] 236: 12 [M::ha_hist_line] 237: * 9 [M::ha_hist_line] 238: * 6 [M::ha_hist_line] 239: 9 [M::ha_hist_line] 240: * 18 [M::ha_hist_line] 241: 7 [M::ha_hist_line] 242: ** 13 [M::ha_hist_line] 243: 7 [M::ha_hist_line] 244: 6 [M::ha_hist_line] 245: 8 [M::ha_hist_line] 246: * 7 [M::ha_hist_line] 247: 5 [M::ha_hist_line] 248: 6 [M::ha_hist_line] 249: 7 [M::ha_hist_line] 250: * 4 [M::ha_hist_line] rest: ****> 390 [M::ha_analyze_count] left: count[7] = 289 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 42; peak_het: 7 [M::ha_ct_shrink::41.91812.83] ==> counted 32360 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2671240 minimizers [M::ha_pt_gen::42.34412.81] ==> indexed 2666979 positions, counted 32360 distinct minimizer k-mers [M::ha_assemble::62.03115.72@16.483GB] ==> corrected reads for round 2 [M::ha_assemble] # bases: 100594571; # corrected bases: 7379; # recorrected bases: 230 [M::ha_assemble] size of buffer: 0.634GB [M::yak_count] collected 2671307 minimizers [M::ha_pt_gen::62.46815.68] ==> counted 35736 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 254 [M::ha_analyze_count] highest: count[41] = 339 [M::ha_hist_line] 1: ****> 3559 [M::ha_hist_line] 2: ****> 964 [M::ha_hist_line] 3: ****> 546 [M::ha_hist_line] 4: ****> 367 [M::ha_hist_line] 5: ** 305 [M::ha_hist_line] 6: ***** 254 [M::ha_hist_line] 7: ** 292 [M::ha_hist_line] 8: * 187 [M::ha_hist_line] 9: *** 221 [M::ha_hist_line] 10: **** 205 [M::ha_hist_line] 11: ** 170 [M::ha_hist_line] 12: * 174 [M::ha_hist_line] 13: *** 180 [M::ha_hist_line] 14: ** 156 [M::ha_hist_line] 15: ** 143 [M::ha_hist_line] 16: **** 186 [M::ha_hist_line] 17: 172 [M::ha_hist_line] 18: ***** 213 [M::ha_hist_line] 19: ** 128 [M::ha_hist_line] 20: * 173 [M::ha_hist_line] 21: *** 166 [M::ha_hist_line] 22: * 145 [M::ha_hist_line] 23: * 127 [M::ha_hist_line] 24: ** 169 [M::ha_hist_line] 25: ***** 139 [M::ha_hist_line] 26: ** 143 [M::ha_hist_line] 27: ** 102 [M::ha_hist_line] 28: **** 110 [M::ha_hist_line] 29: ** 115 [M::ha_hist_line] 30: **** 122 [M::ha_hist_line] 31: * 120 [M::ha_hist_line] 32: **** 122 [M::ha_hist_line] 33: *** 165 [M::ha_hist_line] 34: 207 [M::ha_hist_line] 35: 207 [M::ha_hist_line] 36: **** 162 [M::ha_hist_line] 37: ** 184 [M::ha_hist_line] 38: *** 240 [M::ha_hist_line] 39: * 166 [M::ha_hist_line] 40: ** 277 [M::ha_hist_line] 41: **** 339 [M::ha_hist_line] 42: ** 331 [M::ha_hist_line] 43: ***** 262 [M::ha_hist_line] 44: **** 229 [M::ha_hist_line] 45: ** 237 [M::ha_hist_line] 46: **** 230 [M::ha_hist_line] 47: * 208 [M::ha_hist_line] 48: ***** 239 [M::ha_hist_line] 49: * 200 [M::ha_hist_line] 50: * 213 [M::ha_hist_line] 51: ** 205 [M::ha_hist_line] 52: * 208 [M::ha_hist_line] 53: **** 201 [M::ha_hist_line] 54: 185 [M::ha_hist_line] 55: * 187 [M::ha_hist_line] 56: **** 163 [M::ha_hist_line] 57: *** 219 [M::ha_hist_line] 58: * 180 [M::ha_hist_line] 59: *** 227 [M::ha_hist_line] 60: **** 202 [M::ha_hist_line] 61: ** 184 [M::ha_hist_line] 62: **** 191 [M::ha_hist_line] 63: ** 186 [M::ha_hist_line] 64: 181 [M::ha_hist_line] 65: ** 198 [M::ha_hist_line] 66: ** 209 [M::ha_hist_line] 67: **** 232 [M::ha_hist_line] 68: * 240 [M::ha_hist_line] 69: **** 252 [M::ha_hist_line] 70: * 235 [M::ha_hist_line] 71: ** 251 [M::ha_hist_line] 72: ** 250 [M::ha_hist_line] 73: ** 225 [M::ha_hist_line] 74: ** 210 [M::ha_hist_line] 75: **** 205 [M::ha_hist_line] 76: *** 215 [M::ha_hist_line] 77: **** 217 [M::ha_hist_line] 78: * 181 [M::ha_hist_line] 79: ** 198 [M::ha_hist_line] 80: **** 202 [M::ha_hist_line] 81: ** 264 [M::ha_hist_line] 82: **** 270 [M::ha_hist_line] 83: * 221 [M::ha_hist_line] 84: **** 216 [M::ha_hist_line] 85: ** 237 [M::ha_hist_line] 86: * 219 [M::ha_hist_line] 87: *** 240 [M::ha_hist_line] 88: * 222 [M::ha_hist_line] 89: * 174 [M::ha_hist_line] 90: *** 193 [M::ha_hist_line] 91: **** 150 [M::ha_hist_line] 92: ** 184 [M::ha_hist_line] 93: **** 202 [M::ha_hist_line] 94: * 214 [M::ha_hist_line] 95: *** 262 [M::ha_hist_line] 96: ** 210 [M::ha_hist_line] 97: * 161 [M::ha_hist_line] 98: **** 229 [M::ha_hist_line] 99: *** 233 [M::ha_hist_line] 100: **** 244 [M::ha_hist_line] 101: ** 220 [M::ha_hist_line] 102: 213 [M::ha_hist_line] 103: ** 211 [M::ha_hist_line] 104: ** 182 [M::ha_hist_line] 105: ** 209 [M::ha_hist_line] 106: * 187 [M::ha_hist_line] 107: ** 223 [M::ha_hist_line] 108: ** 236 [M::ha_hist_line] 109: ***** 226 [M::ha_hist_line] 110: **** 200 [M::ha_hist_line] 111: 186 [M::ha_hist_line] 112: * 254 [M::ha_hist_line] 113: ***** 295 [M::ha_hist_line] 114: ** 250 [M::ha_hist_line] 115: ***** 246 [M::ha_hist_line] 116: ** 238 [M::ha_hist_line] 117: ** 210 [M::ha_hist_line] 118: * 206 [M::ha_hist_line] 119: ** 211 [M::ha_hist_line] 120: ** 224 [M::ha_hist_line] 121: ** 183 [M::ha_hist_line] 122: **** 189 [M::ha_hist_line] 123: **** 175 [M::ha_hist_line] 124: **** 176 [M::ha_hist_line] 125: ***** 174 [M::ha_hist_line] 126: **** 163 [M::ha_hist_line] 127: * 145 [M::ha_hist_line] 128: * 146 [M::ha_hist_line] 129: **** 155 [M::ha_hist_line] 130: ** 169 [M::ha_hist_line] 131: ** 155 [M::ha_hist_line] 132: **** 164 [M::ha_hist_line] 133: * 140 [M::ha_hist_line] 134: **** 123 [M::ha_hist_line] 135: **** 108 [M::ha_hist_line] 136: ** 115 [M::ha_hist_line] 137: * 117 [M::ha_hist_line] 138: ** 109 [M::ha_hist_line] 139: **** 110 [M::ha_hist_line] 140: * 111 [M::ha_hist_line] 141: **** 109 [M::ha_hist_line] 142: *** 93 [M::ha_hist_line] 143: ** 87 [M::ha_hist_line] 144: ** 74 [M::ha_hist_line] 145: **** 80 [M::ha_hist_line] 146: * 57 [M::ha_hist_line] 147: * 71 [M::ha_hist_line] 148: ** 60 [M::ha_hist_line] 149: * 72 [M::ha_hist_line] 150: **** 55 [M::ha_hist_line] 151: ** 47 [M::ha_hist_line] 152: **** 39 [M::ha_hist_line] 153: * 56 [M::ha_hist_line] 154: *** 65 [M::ha_hist_line] 155: *** 56 [M::ha_hist_line] 156: ** 61 [M::ha_hist_line] 157: ** 47 [M::ha_hist_line] 158: ** 34 [M::ha_hist_line] 159: **** 40 [M::ha_hist_line] 160: ** 34 [M::ha_hist_line] 161: ** 35 [M::ha_hist_line] 162: * 37 [M::ha_hist_line] 163: 37 [M::ha_hist_line] 164: 38 [M::ha_hist_line] 165: * 44 [M::ha_hist_line] 166: ** 35 [M::ha_hist_line] 167: * 32 [M::ha_hist_line] 168: * 45 [M::ha_hist_line] 169: ** 53 [M::ha_hist_line] 170: * 37 [M::ha_hist_line] 171: **** 26 [M::ha_hist_line] 172: * 43 [M::ha_hist_line] 173: **** 42 [M::ha_hist_line] 174: ** 49 [M::ha_hist_line] 175: **** 54 [M::ha_hist_line] 176: * 32 [M::ha_hist_line] 177: **** 54 [M::ha_hist_line] 178: **** 41 [M::ha_hist_line] 179: ** 33 [M::ha_hist_line] 180: * 30 [M::ha_hist_line] 181: ** 48 [M::ha_hist_line] 182: *** 50 [M::ha_hist_line] 183: * 31 [M::ha_hist_line] 184: **** 39 [M::ha_hist_line] 185: ** 33 [M::ha_hist_line] 186: ** 47 [M::ha_hist_line] 187: ** 49 [M::ha_hist_line] 188: **** 41 [M::ha_hist_line] 189: * 31 [M::ha_hist_line] 190: ***** 45 [M::ha_hist_line] 191: * 17 [M::ha_hist_line] 192: **** 27 [M::ha_hist_line] 193: * 24 [M::ha_hist_line] 194: *** 32 [M::ha_hist_line] 195: * 31 [M::ha_hist_line] 196: ** 33 [M::ha_hist_line] 197: ** 19 [M::ha_hist_line] 198: * 16 [M::ha_hist_line] 199: * 11 [M::ha_hist_line] 200: * 14 [M::ha_hist_line] 201: 4 [M::ha_hist_line] 202: 12 [M::ha_hist_line] 203: ** 13 [M::ha_hist_line] 204: **** 16 [M::ha_hist_line] 205: 11 [M::ha_hist_line] 206: * 11 [M::ha_hist_line] 207: **** 26 [M::ha_hist_line] 208: * 9 [M::ha_hist_line] 209: 7 [M::ha_hist_line] 210: ** 15 [M::ha_hist_line] 211: * 10 [M::ha_hist_line] 212: 8 [M::ha_hist_line] 213: ** 14 [M::ha_hist_line] 214: * 10 [M::ha_hist_line] 215: 10 [M::ha_hist_line] 216: 11 [M::ha_hist_line] 217: 8 [M::ha_hist_line] 218: * 4 [M::ha_hist_line] 219: *** 18 [M::ha_hist_line] 220: ** 12 [M::ha_hist_line] 221: 8 [M::ha_hist_line] 222: ** 15 [M::ha_hist_line] 223: ** 10 [M::ha_hist_line] 224: 9 [M::ha_hist_line] 225: * 4 [M::ha_hist_line] 226: 6 [M::ha_hist_line] 227: 3 [M::ha_hist_line] 228: 9 [M::ha_hist_line] 229: 6 [M::ha_hist_line] 230: 6 [M::ha_hist_line] 231: 7 [M::ha_hist_line] 232: 7 [M::ha_hist_line] 233: 10 [M::ha_hist_line] 234: 5 [M::ha_hist_line] 235: 7 [M::ha_hist_line] 236: 11 [M::ha_hist_line] 237: 9 [M::ha_hist_line] 238: 7 [M::ha_hist_line] 239: * 9 [M::ha_hist_line] 240: ** 15 [M::ha_hist_line] 241: * 10 [M::ha_hist_line] 242: ** 13 [M::ha_hist_line] 243: 7 [M::ha_hist_line] 244: 6 [M::ha_hist_line] 245: 6 [M::ha_hist_line] 246: 7 [M::ha_hist_line] 247: 7 [M::ha_hist_line] 248: 6 [M::ha_hist_line] 249: 7 [M::ha_hist_line] 250: * 4 [M::ha_hist_line] rest: ****> 390 [M::ha_analyze_count] left: count[7] = 292 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 41; peak_het: 7 [M::ha_ct_shrink::62.48615.67] ==> counted 32177 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2671307 minimizers [M::ha_pt_gen::62.90115.64] ==> indexed 2667748 positions, counted 32177 distinct minimizer k-mers [M::ha_assemble::87.13616.40@16.483GB] ==> corrected reads for round 3 [M::ha_assemble] # bases: 100597775; # corrected bases: 987; # recorrected bases: 76 [M::ha_assemble] size of buffer: 0.622GB [M::yak_count] collected 2671264 minimizers [M::ha_pt_gen::87.59816.36] ==> counted 35677 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 255 [M::ha_analyze_count] highest: count[41] = 339 [M::ha_hist_line] 1: ****> 3525 [M::ha_hist_line] 2: ****> 954 [M::ha_hist_line] 3: ****> 543 [M::ha_hist_line] 4: ****> 362 [M::ha_hist_line] 5: *** 303 [M::ha_hist_line] 6: * 255 [M::ha_hist_line] 7: *** 288 [M::ha_hist_line] 8: * 186 [M::ha_hist_line] 9: *** 221 [M::ha_hist_line] 10: **** 205 [M::ha_hist_line] 11: ** 170 [M::ha_hist_line] 12: * 174 [M::ha_hist_line] 13: *** 180 [M::ha_hist_line] 14: ** 156 [M::ha_hist_line] 15: * 145 [M::ha_hist_line] 16: * 186 [M::ha_hist_line] 17: ** 171 [M::ha_hist_line] 18: ***** 213 [M::ha_hist_line] 19: * 127 [M::ha_hist_line] 20: *** 173 [M::ha_hist_line] 21: *** 165 [M::ha_hist_line] 22: * 145 [M::ha_hist_line] 23: * 127 [M::ha_hist_line] 24: ** 170 [M::ha_hist_line] 25: ***** 138 [M::ha_hist_line] 26: ** 143 [M::ha_hist_line] 27: ** 102 [M::ha_hist_line] 28: * 112 [M::ha_hist_line] 29: ** 114 [M::ha_hist_line] 30: **** 121 [M::ha_hist_line] 31: *** 120 [M::ha_hist_line] 32: * 124 [M::ha_hist_line] 33: **** 163 [M::ha_hist_line] 34: ** 210 [M::ha_hist_line] 35: ***** 207 [M::ha_hist_line] 36: * 158 [M::ha_hist_line] 37: ***** 185 [M::ha_hist_line] 38: *** 240 [M::ha_hist_line] 39: * 166 [M::ha_hist_line] 40: ** 277 [M::ha_hist_line] 41: **** 339 [M::ha_hist_line] 42: *** 328 [M::ha_hist_line] 43: ** 265 [M::ha_hist_line] 44: * 227 [M::ha_hist_line] 45: *** 240 [M::ha_hist_line] 46: **** 229 [M::ha_hist_line] 47: * 208 [M::ha_hist_line] 48: ***** 239 [M::ha_hist_line] 49: * 200 [M::ha_hist_line] 50: ***** 212 [M::ha_hist_line] 51: **** 203 [M::ha_hist_line] 52: ** 210 [M::ha_hist_line] 53: **** 202 [M::ha_hist_line] 54: * 185 [M::ha_hist_line] 55: * 187 [M::ha_hist_line] 56: **** 163 [M::ha_hist_line] 57: *** 219 [M::ha_hist_line] 58: * 180 [M::ha_hist_line] 59: *** 227 [M::ha_hist_line] 60: **** 202 [M::ha_hist_line] 61: ** 183 [M::ha_hist_line] 62: ** 192 [M::ha_hist_line] 63: 186 [M::ha_hist_line] 64: * 181 [M::ha_hist_line] 65: *** 199 [M::ha_hist_line] 66: **** 205 [M::ha_hist_line] 67: * 234 [M::ha_hist_line] 68: *** 240 [M::ha_hist_line] 69: ** 252 [M::ha_hist_line] 70: * 235 [M::ha_hist_line] 71: **** 252 [M::ha_hist_line] 72: ** 250 [M::ha_hist_line] 73: * 226 [M::ha_hist_line] 74: ** 209 [M::ha_hist_line] 75: **** 205 [M::ha_hist_line] 76: * 215 [M::ha_hist_line] 77: *** 219 [M::ha_hist_line] 78: * 179 [M::ha_hist_line] 79: ** 198 [M::ha_hist_line] 80: **** 202 [M::ha_hist_line] 81: ** 264 [M::ha_hist_line] 82: **** 272 [M::ha_hist_line] 83: ***** 219 [M::ha_hist_line] 84: **** 216 [M::ha_hist_line] 85: ** 238 [M::ha_hist_line] 86: **** 218 [M::ha_hist_line] 87: ***** 239 [M::ha_hist_line] 88: ** 223 [M::ha_hist_line] 89: * 174 [M::ha_hist_line] 90: * 193 [M::ha_hist_line] 91: ** 150 [M::ha_hist_line] 92: * 185 [M::ha_hist_line] 93: * 201 [M::ha_hist_line] 94: ***** 213 [M::ha_hist_line] 95: *** 262 [M::ha_hist_line] 96: ** 210 [M::ha_hist_line] 97: * 160 [M::ha_hist_line] 98: * 227 [M::ha_hist_line] 99: *** 235 [M::ha_hist_line] 100: *** 241 [M::ha_hist_line] 101: * 221 [M::ha_hist_line] 102: * 215 [M::ha_hist_line] 103: ** 210 [M::ha_hist_line] 104: ** 182 [M::ha_hist_line] 105: * 212 [M::ha_hist_line] 106: * 187 [M::ha_hist_line] 107: *** 222 [M::ha_hist_line] 108: ** 237 [M::ha_hist_line] 109: ***** 226 [M::ha_hist_line] 110: * 200 [M::ha_hist_line] 111: * 186 [M::ha_hist_line] 112: ** 252 [M::ha_hist_line] 113: ***** 296 [M::ha_hist_line] 114: 249 [M::ha_hist_line] 115: 248 [M::ha_hist_line] 116: ** 238 [M::ha_hist_line] 117: ** 210 [M::ha_hist_line] 118: *** 206 [M::ha_hist_line] 119: ** 211 [M::ha_hist_line] 120: ** 224 [M::ha_hist_line] 121: ** 183 [M::ha_hist_line] 122: **** 189 [M::ha_hist_line] 123: **** 175 [M::ha_hist_line] 124: **** 176 [M::ha_hist_line] 125: * 174 [M::ha_hist_line] 126: **** 163 [M::ha_hist_line] 127: ** 144 [M::ha_hist_line] 128: *** 145 [M::ha_hist_line] 129: ** 156 [M::ha_hist_line] 130: ** 169 [M::ha_hist_line] 131: ** 155 [M::ha_hist_line] 132: **** 162 [M::ha_hist_line] 133: **** 137 [M::ha_hist_line] 134: * 124 [M::ha_hist_line] 135: * 111 [M::ha_hist_line] 136: *** 117 [M::ha_hist_line] 137: ** 114 [M::ha_hist_line] 138: * 111 [M::ha_hist_line] 139: **** 109 [M::ha_hist_line] 140: * 113 [M::ha_hist_line] 141: **** 107 [M::ha_hist_line] 142: **** 94 [M::ha_hist_line] 143: ** 88 [M::ha_hist_line] 144: ** 73 [M::ha_hist_line] 145: **** 80 [M::ha_hist_line] 146: * 57 [M::ha_hist_line] 147: ***** 72 [M::ha_hist_line] 148: * 59 [M::ha_hist_line] 149: ***** 70 [M::ha_hist_line] 150: **** 56 [M::ha_hist_line] 151: 45 [M::ha_hist_line] 152: **** 41 [M::ha_hist_line] 153: * 56 [M::ha_hist_line] 154: *** 65 [M::ha_hist_line] 155: *** 58 [M::ha_hist_line] 156: ** 61 [M::ha_hist_line] 157: ** 47 [M::ha_hist_line] 158: ** 34 [M::ha_hist_line] 159: **** 40 [M::ha_hist_line] 160: ** 34 [M::ha_hist_line] 161: ** 34 [M::ha_hist_line] 162: * 38 [M::ha_hist_line] 163: 37 [M::ha_hist_line] 164: 36 [M::ha_hist_line] 165: * 45 [M::ha_hist_line] 166: ** 35 [M::ha_hist_line] 167: * 31 [M::ha_hist_line] 168: * 45 [M::ha_hist_line] 169: ** 49 [M::ha_hist_line] 170: **** 41 [M::ha_hist_line] 171: **** 27 [M::ha_hist_line] 172: **** 42 [M::ha_hist_line] 173: * 43 [M::ha_hist_line] 174: ** 49 [M::ha_hist_line] 175: **** 54 [M::ha_hist_line] 176: ** 33 [M::ha_hist_line] 177: **** 54 [M::ha_hist_line] 178: **** 41 [M::ha_hist_line] 179: ** 33 [M::ha_hist_line] 180: * 30 [M::ha_hist_line] 181: ** 48 [M::ha_hist_line] 182: *** 50 [M::ha_hist_line] 183: * 31 [M::ha_hist_line] 184: **** 39 [M::ha_hist_line] 185: ** 33 [M::ha_hist_line] 186: ** 47 [M::ha_hist_line] 187: ** 49 [M::ha_hist_line] 188: **** 41 [M::ha_hist_line] 189: * 31 [M::ha_hist_line] 190: ***** 45 [M::ha_hist_line] 191: * 17 [M::ha_hist_line] 192: **** 27 [M::ha_hist_line] 193: * 24 [M::ha_hist_line] 194: *** 32 [M::ha_hist_line] 195: * 31 [M::ha_hist_line] 196: ** 33 [M::ha_hist_line] 197: ** 19 [M::ha_hist_line] 198: * 16 [M::ha_hist_line] 199: * 11 [M::ha_hist_line] 200: * 14 [M::ha_hist_line] 201: 4 [M::ha_hist_line] 202: 12 [M::ha_hist_line] 203: ** 13 [M::ha_hist_line] 204: **** 16 [M::ha_hist_line] 205: 11 [M::ha_hist_line] 206: * 11 [M::ha_hist_line] 207: **** 26 [M::ha_hist_line] 208: * 9 [M::ha_hist_line] 209: 7 [M::ha_hist_line] 210: ** 15 [M::ha_hist_line] 211: * 10 [M::ha_hist_line] 212: 8 [M::ha_hist_line] 213: ** 14 [M::ha_hist_line] 214: * 10 [M::ha_hist_line] 215: 10 [M::ha_hist_line] 216: 11 [M::ha_hist_line] 217: 8 [M::ha_hist_line] 218: * 4 [M::ha_hist_line] 219: *** 18 [M::ha_hist_line] 220: ** 12 [M::ha_hist_line] 221: 8 [M::ha_hist_line] 222: ** 15 [M::ha_hist_line] 223: ** 10 [M::ha_hist_line] 224: 9 [M::ha_hist_line] 225: * 4 [M::ha_hist_line] 226: 6 [M::ha_hist_line] 227: 3 [M::ha_hist_line] 228: 9 [M::ha_hist_line] 229: 6 [M::ha_hist_line] 230: 6 [M::ha_hist_line] 231: 7 [M::ha_hist_line] 232: 7 [M::ha_hist_line] 233: 10 [M::ha_hist_line] 234: 5 [M::ha_hist_line] 235: 7 [M::ha_hist_line] 236: 11 [M::ha_hist_line] 237: 9 [M::ha_hist_line] 238: 7 [M::ha_hist_line] 239: * 9 [M::ha_hist_line] 240: ** 15 [M::ha_hist_line] 241: * 10 [M::ha_hist_line] 242: ** 13 [M::ha_hist_line] 243: 7 [M::ha_hist_line] 244: 6 [M::ha_hist_line] 245: 6 [M::ha_hist_line] 246: 7 [M::ha_hist_line] 247: 7 [M::ha_hist_line] 248: 6 [M::ha_hist_line] 249: 7 [M::ha_hist_line] 250: * 4 [M::ha_hist_line] rest: ****> 390 [M::ha_analyze_count] left: count[7] = 288 [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 41; peak_het: 7 [M::ha_ct_shrink::87.61716.36] ==> counted 32152 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2671264 minimizers [M::ha_pt_gen::88.08516.32] ==> indexed 2667739 positions, counted 32152 distinct minimizer k-mers [M::ha_assemble::93.465*16.60@16.483GB] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 3951894 [M::ha_print_ovlp_stat] # strong overlaps: 1885331 [M::ha_print_ovlp_stat] # weak overlaps: 2066563 [M::ha_print_ovlp_stat] # exact overlaps: 3897966 [M::ha_print_ovlp_stat] # inexact overlaps: 53928 [M::ha_print_ovlp_stat] # overlaps without large indels: 3951490 [M::ha_print_ovlp_stat] # reverse overlaps: 491953 [M::ha_opt_update_cov_min] updated max_n_chain to 41000 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: 40 [M::purge_dups] purge duplication coverage threshold: 51 [M::ug_ext_gfa::] # tips::9 Writing raw unitig GFA to disk... Writing processed unitig GFA to disk... [M::purge_dups] homozygous read coverage threshold: 40 [M::purge_dups] purge duplication coverage threshold: 51 [M::mc_solve:: # edges: 0] [M::mc_solve_core_adv::0.000] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [34, infinity] Writing primary contig GFA to disk... Writing alternate contig GFA to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.19.8-r603 [M::main] CMD: /u/project/geschwind/leqi0001/software/hifiasm/hifiasm -o /u/project/geschwind/leqi0001/longreads/assembly_phased/GIH.92.C2.hap1 -t 32 --primary --hg-size 2m -D 1000 -N 20000 GIH.92.C2.hap1.fastq.gz [M::main] Real time: 100.692 sec; CPU: 1557.883 sec; Peak RSS: 16.483 GB [M::ha_analyze_count] lowest: count[6] = 7905 [M::ha_analyze_count] highest: count[7] = 8120 [M::ha_hist_line] 2: ****> 92907 [M::ha_hist_line] 3: ****> 21567 [M::ha_hist_line] 4: ****> 12721 [M::ha_hist_line] 5: ****> 9037 [M::ha_hist_line] 6: ***** 7905 [M::ha_hist_line] 7: **** 8120 [M::ha_hist_line] 8: * 4926 [M::ha_hist_line] 9: * 5744 [M::ha_hist_line] 10: **** 6182 [M::ha_hist_line] 11: * 5443 [M::ha_hist_line] 12: 5735 [M::ha_hist_line] 13: 5786 [M::ha_hist_line] 14: * 4281 [M::ha_hist_line] 15: *** 5104 [M::ha_hist_line] 16: **** 4866 [M::ha_hist_line] 17: * 3489 [M::ha_hist_line] 18: *** 4646 [M::ha_hist_line] 19: **** 3890 [M::ha_hist_line] 20: **** 4585 [M::ha_hist_line] 21: *** 4491 [M::ha_hist_line] 22: * 3319 [M::ha_hist_line] 23: ** 4150 [M::ha_hist_line] 24: 3970 [M::ha_hist_line] 25: ** 3763 [M::ha_hist_line] 26: * 4008 [M::ha_hist_line] 27: **** 4840 [M::ha_hist_line] 28: ** 4403 [M::ha_hist_line] 29: *** 4806 [M::ha_hist_line] 30: ** 3755 [M::ha_hist_line] 31: * 4267 [M::ha_hist_line] 32: *** 4436 [M::ha_hist_line] 33: * 4661 [M::ha_hist_line] 34: ** 5322 [M::ha_hist_line] 35: *** 6734 [M::ha_hist_line] 36: * 6377 [M::ha_hist_line] 37: ** 6372 [M::ha_hist_line] 38: * 6446 [M::ha_hist_line] 39: ***** 6429 [M::ha_hist_line] 40: **** 6205 [M::ha_hist_line] 41: * 5789 [M::ha_hist_line] 42: 6587 [M::ha_hist_line] 43: 6558 [M::ha_hist_line] 44: * 5952 [M::ha_hist_line] 45: ** 5646 [M::ha_hist_line] 46: *** 6111 [M::ha_hist_line] 47: 5739 [M::ha_hist_line] 48: 5731 [M::ha_hist_line] 49: **** 5884 [M::ha_hist_line] 50: * 5444 [M::ha_hist_line] 51: **** 5558 [M::ha_hist_line] 52: *** 5959 [M::ha_hist_line] 53: *** 6265 [M::ha_hist_line] 54: ** 5037 [M::ha_hist_line] 55: * 5124 [M::ha_hist_line] 56: **** 5823 [M::ha_hist_line] 57: ** 5978 [M::ha_hist_line] 58: *** 6282 [M::ha_hist_line] 59: * 5787 [M::ha_hist_line] 60: *** 6060 [M::ha_hist_line] 61: * 5571 [M::ha_hist_line] 62: 5915 [M::ha_hist_line] 63: 5899 [M::ha_hist_line] 64: ***** 6402 [M::ha_hist_line] 65: * 5443 [M::ha_hist_line] 66: **** 5546 [M::ha_hist_line] 67: ** 5319 [M::ha_hist_line] 68: * 6291 [M::ha_hist_line] 69: **** 5826 [M::ha_hist_line] 70: **** 5538 [M::ha_hist_line] 71: **** 5854 [M::ha_hist_line] 72: ** 6029 [M::ha_hist_line] 73: * 6217 [M::ha_hist_line] 74: ** 6335 [M::ha_hist_line] 75: ** 6369 [M::ha_hist_line] 76: * 6083 [M::ha_hist_line] 77: **** 6835 [M::ha_hist_line] 78: *** 6879 [M::ha_hist_line] 79: ** 6040 [M::ha_hist_line] 80: 6050 [M::ha_hist_line] 81: 6111 [M::ha_hist_line] 82: ** 5377 [M::ha_hist_line] 83: * 4751 [M::ha_hist_line] 84: *** 4947 [M::ha_hist_line] 85: * 4939 [M::ha_hist_line] 86: ** 5034 [M::ha_hist_line] 87: * 4943 [M::ha_hist_line] 88: **** 5162 [M::ha_hist_line] 89: * 5923 [M::ha_hist_line] 90: **** 6161 [M::ha_hist_line] 91: *** 6081 [M::ha_hist_line] 92: * 5570 [M::ha_hist_line] 93: *** 6052 [M::ha_hist_line] 94: * 6104 [M::ha_hist_line] 95: **** 6138 [M::ha_hist_line] 96: * 5781 [M::ha_hist_line] 97: **** 5562 [M::ha_hist_line] 98: **** 5885 [M::ha_hist_line] 99: * 5763 [M::ha_hist_line] 100: ** 5550 [M::ha_hist_line] 101: ** 5687 [M::ha_hist_line] 102: **** 5167 [M::ha_hist_line] 103: **** 5560 [M::ha_hist_line] 104: ** 5688 [M::ha_hist_line] 105: * 5615 [M::ha_hist_line] 106: * 5304 [M::ha_hist_line] 107: *** 5421 [M::ha_hist_line] 108: **** 6147 [M::ha_hist_line] 109: ** 5710 [M::ha_hist_line] 110: *** 5101 [M::ha_hist_line] 111: **** 4885 [M::ha_hist_line] 112: ** 4020 [M::ha_hist_line] 113: ** 4036 [M::ha_hist_line] 114: * 4317 [M::ha_hist_line] 115: * 3940 [M::ha_hist_line] 116: *** 4441 [M::ha_hist_line] 117: ** 4369 [M::ha_hist_line] 118: ** 3746 [M::ha_hist_line] 119: 3633 [M::ha_hist_line] 120: 3617 [M::ha_hist_line] 121: **** 3544 [M::ha_hist_line] 122: ** 3088 [M::ha_hist_line] 123: 3644 [M::ha_hist_line] 124: 3647 [M::ha_hist_line] 125: * 3474 [M::ha_hist_line] 126: **** 3260 [M::ha_hist_line] 127: * 3181 [M::ha_hist_line] 128: **** 3588 [M::ha_hist_line] 129: ** 3393 [M::ha_hist_line] 130: ***** 3201 [M::ha_hist_line] 131: ** 3124 [M::ha_hist_line] 132: * 2540 [M::ha_hist_line] 133: ** 2438 [M::ha_hist_line] 134: ***** 2681 [M::ha_hist_line] 135: ** 2730 [M::ha_hist_line] 136: **** 2623 [M::ha_hist_line] 137: ** 2726 [M::ha_hist_line] 138: **** 2560 [M::ha_hist_line] 139: ** 2447 [M::ha_hist_line] 140: * 2025 [M::ha_hist_line] 141: ** 1797 [M::ha_hist_line] 142: ** 1778 [M::ha_hist_line] 143: **** 1630 [M::ha_hist_line] 144: * 1682 [M::ha_hist_line] 145: *** 1874 [M::ha_hist_line] 146: **** 1963 [M::ha_hist_line] 147: ** 1752 [M::ha_hist_line] 148: * 1725 [M::ha_hist_line] 149: **** 1463 [M::ha_hist_line] 150: **** 1630 [M::ha_hist_line] 151: * 1574 [M::ha_hist_line] 152: * 1253 [M::ha_hist_line] 153: ** 1108 [M::ha_hist_line] 154: * 1195 [M::ha_hist_line] 155: * 1088 [M::ha_hist_line] 156: **** 976 [M::ha_hist_line] 157: **** 953 [M::ha_hist_line] 158: **** 960 [M::ha_hist_line] 159: * 1042 [M::ha_hist_line] 160: ** 1157 [M::ha_hist_line] 161: ** 1110 [M::ha_hist_line] 162: **** 999 [M::ha_hist_line] 163: ** 834 [M::ha_hist_line] 164: ** 1139 [M::ha_hist_line] 165: *** 1193 [M::ha_hist_line] 166: ** 1109 [M::ha_hist_line] 167: **** 1259 [M::ha_hist_line] 168: ** 1124 [M::ha_hist_line] 169: ** 1145 [M::ha_hist_line] 170: **** 982 [M::ha_hist_line] 171: **** 686 [M::ha_hist_line] 172: **** 684 [M::ha_hist_line] 173: * 726 [M::ha_hist_line] 174: * 907 [M::ha_hist_line] 175: **** 952 [M::ha_hist_line] 176: ** 811 [M::ha_hist_line] 177: ** 810 [M::ha_hist_line] 178: * 922 [M::ha_hist_line] 179: * 1078 [M::ha_hist_line] 180: ** 974 [M::ha_hist_line] 181: * 887 [M::ha_hist_line] 182: ** 784 [M::ha_hist_line] 183: * 591 [M::ha_hist_line] 184: *** 693 [M::ha_hist_line] 185: **** 622 [M::ha_hist_line] 186: ** 691 [M::ha_hist_line] 187: 586 [M::ha_hist_line] 188: **** 617 [M::ha_hist_line] 189: * 567 [M::ha_hist_line] 190: **** 623 [M::ha_hist_line] 191: **** 630 [M::ha_hist_line] 192: * 591 [M::ha_hist_line] 193: **** 663 [M::ha_hist_line] 194: * 568 [M::ha_hist_line] 195: **** 502 [M::ha_hist_line] 196: 351 [M::ha_hist_line] 197: 343 [M::ha_hist_line] 198: 335 [M::ha_hist_line] 199: 356 [M::ha_hist_line] 200: * 380 [M::ha_hist_line] 201: 370 [M::ha_hist_line] 202: 436 [M::ha_hist_line] 203: ** 470 [M::ha_hist_line] 204: * 416 [M::ha_hist_line] 205: ** 469 [M::ha_hist_line] 206: *** 585 [M::ha_hist_line] 207: ** 485 [M::ha_hist_line] 208: * 396 [M::ha_hist_line] 209: ** 300 [M::ha_hist_line] 210: *** 344 [M::ha_hist_line] 211: 222 [M::ha_hist_line] 212: 275 [M::ha_hist_line] 213: 277 [M::ha_hist_line] 214: 339 [M::ha_hist_line] 215: * 413 [M::ha_hist_line] 216: ** 450 [M::ha_hist_line] 217: * 432 [M::ha_hist_line] 218: 439 [M::ha_hist_line] 219: 404 [M::ha_hist_line] 220: 433 [M::ha_hist_line] 221: 378 [M::ha_hist_line] 222: 241 [M::ha_hist_line] 223: 241 [M::ha_hist_line] 224: * 251 [M::ha_hist_line] 225: *** 289 [M::ha_hist_line] 226: 274 [M::ha_hist_line] 227: 352 [M::ha_hist_line] 228: ** 258 [M::ha_hist_line] 229: 386 [M::ha_hist_line] 230: 338 [M::ha_hist_line] 231: 344 [M::ha_hist_line] 232: 350 [M::ha_hist_line] 233: * 411 [M::ha_hist_line] 234: 321 [M::ha_hist_line] 235: ** 464 [M::ha_hist_line] 236: ** 475 [M::ha_hist_line] 237: ** 468 [M::ha_hist_line] 238: * 424 [M::ha_hist_line] 239: 259 [M::ha_hist_line] 240: 269 [M::ha_hist_line] 241: * 227 [M::ha_hist_line] 242: * 193 [M::ha_hist_line] 243: 226 [M::ha_hist_line] 244: 212 [M::ha_hist_line] 245: 205 [M::ha_hist_line] 246: 200 [M::ha_hist_line] 247: * 215 [M::ha_hist_line] 248: 202 [M::ha_hist_line] 249: * 191 [M::ha_hist_line] 250: 264 [M::ha_hist_line] 251: 278 [M::ha_hist_line] 252: 199 [M::ha_hist_line] 253: 162 [M::ha_hist_line] 254: 149 [M::ha_hist_line] 255: 151 [M::ha_hist_line] 256: 119 [M::ha_hist_line] 257: 119 [M::ha_hist_line] 258: 107 [M::ha_hist_line] 259: 145 [M::ha_hist_line] 260: 164 [M::ha_hist_line] 261: 70 [M::ha_hist_line] 262: 100 [M::ha_hist_line] 263: 130 [M::ha_hist_line] 264: 136 [M::ha_hist_line] 265: 136 [M::ha_hist_line] 266: * 78 [M::ha_hist_line] 267: 135 [M::ha_hist_line] 268: 106 [M::ha_hist_line] 269: 72 [M::ha_hist_line] 270: 78 [M::ha_hist_line] 271: 90 [M::ha_hist_line] 272: 146 [M::ha_hist_line] 273: 118 [M::ha_hist_line] 274: 190 [M::ha_hist_line] 275: 134 [M::ha_hist_line] 276: 131 [M::ha_hist_line] 277: 219 [M::ha_hist_line] 278: * 262 [M::ha_hist_line] 279: 134 [M::ha_hist_line] 280: 187 [M::ha_hist_line] 281: * 123 [M::ha_hist_line] 282: 109 [M::ha_hist_line] 283: 145 [M::ha_hist_line] 284: 122 [M::ha_hist_line] 285: 93 [M::ha_hist_line] 286: 88 [M::ha_hist_line] 287: 86 [M::ha_hist_line] 288: 82 [M::ha_hist_line] 289: 79 [M::ha_hist_line] 290: 51 [M::ha_hist_line] 291: 70 [M::ha_hist_line] 292: 63 [M::ha_hist_line] 293: 50 [M::ha_hist_line] 294: 48 [M::ha_hist_line] rest: ** 8106 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 50; peak_het: 7 [M::ha_ct_shrink::15.1481.70] ==> counted 2 distinct minimizer k-mers [M::ha_ft_gen::15.1611.69@16.468GB] ==> filtered out 2 k-mers occurring 4094 or more times [M::ha_opt_update_cov] updated max_n_chain to 50000 [M::yak_count] collected 2686566 minimizers [M::ha_pt_gen::16.450*1.90] ==> counted 90579 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[8] = 207 [M::ha_analyze_count] highest: count[77] = 280 [M::ha_hist_line] 1: ****> 53355 [M::ha_hist_line] 2: ****> 4842 [M::ha_hist_line] 3: ****> 1201 [M::ha_hist_line] 4: ****> 625 [M::ha_hist_line] 5: ****> 397 [M::ha_hist_line] 6: ****> 343 [M::ha_hist_line] 7: ****> 330 [M::ha_hist_line] 8: ** 207 [M::ha_hist_line] 9: **** 223 [M::ha_hist_line] 10: ***** 250 [M::ha_hist_line] 11: * 215 [M::ha_hist_line] 12: *** 227 [M::ha_hist_line] 13: **** 212 [M::ha_hist_line] 14: * 176 [M::ha_hist_line] 15: *** 205 [M::ha_hist_line] 16: * 188 [M::ha_hist_line] 17: ** 130 [M::ha_hist_line] 18: *** 192 [M::ha_hist_line] 19: * 154 [M::ha_hist_line] 20: ** 185 [M::ha_hist_line] 21: ** 184 [M::ha_hist_line] 22: ** 140 [M::ha_hist_line] 23: ** 162 [M::ha_hist_line] 24: **** 147 [M::ha_hist_line] 25: **** 135 [M::ha_hist_line] 26: **** 180 [M::ha_hist_line] 27: ** 173 [M::ha_hist_line] 28: * 200 [M::ha_hist_line] 29: **** 158 [M::ha_hist_line] 30: ** 150 [M::ha_hist_line] 31: **** 167 [M::ha_hist_line] 32: **** 178 [M::ha_hist_line] 33: ** 207 [M::ha_hist_line] 34: ***** 220 [M::ha_hist_line] 35: ***** 271 [M::ha_hist_line] 36: * 237 [M::ha_hist_line] 37: **** 257 [M::ha_hist_line] 38: **** 246 [M::ha_hist_line] 39: ** 275 [M::ha_hist_line] 40: * 216 [M::ha_hist_line] 41: ***** 250 [M::ha_hist_line] 42: *** 278 [M::ha_hist_line] 43: **** 234 [M::ha_hist_line] 44: ** 229 [M::ha_hist_line] 45: * 238 [M::ha_hist_line] 46: ** 241 [M::ha_hist_line] 47: ** 231 [M::ha_hist_line] 48: *** 232 [M::ha_hist_line] 49: * 217 [M::ha_hist_line] 50: **** 225 [M::ha_hist_line] 51: *** 237 [M::ha_hist_line] 52: **** 225 [M::ha_hist_line] 53: ** 231 [M::ha_hist_line] 54: * 210 [M::ha_hist_line] 55: ** 219 [M::ha_hist_line] 56: **** 224 [M::ha_hist_line] 57: ** 240 [M::ha_hist_line] 58: **** 238 [M::ha_hist_line] 59: 228 [M::ha_hist_line] 60: ** 241 [M::ha_hist_line] 61: *** 239 [M::ha_hist_line] 62: **** 246 [M::ha_hist_line] 63: * 211 [M::ha_hist_line] 64: ** 241 [M::ha_hist_line] 65: **** 212 [M::ha_hist_line] 66: **** 213 [M::ha_hist_line] 67: **** 225 [M::ha_hist_line] 68: * 243 [M::ha_hist_line] 69: **** 231 [M::ha_hist_line] 70: * 237 [M::ha_hist_line] 71: * 215 [M::ha_hist_line] 72: ** 231 [M::ha_hist_line] 73: *** 267 [M::ha_hist_line] 74: **** 257 [M::ha_hist_line] 75: ** 241 [M::ha_hist_line] 76: ** 264 [M::ha_hist_line] 77: **** 280 [M::ha_hist_line] 78: *** 250 [M::ha_hist_line] 79: **** 235 [M::ha_hist_line] 80: **** 247 [M::ha_hist_line] 81: ** 207 [M::ha_hist_line] 82: * 199 [M::ha_hist_line] 83: ** 206 [M::ha_hist_line] 84: * 181 [M::ha_hist_line] 85: ** 184 [M::ha_hist_line] 86: ** 196 [M::ha_hist_line] 87: *** 209 [M::ha_hist_line] 88: **** 212 [M::ha_hist_line] 89: ** 251 [M::ha_hist_line] 90: ** 218 [M::ha_hist_line] 91: ***** 249 [M::ha_hist_line] 92: ** 231 [M::ha_hist_line] 93: **** 246 [M::ha_hist_line] 94: * 216 [M::ha_hist_line] 95: ** 227 [M::ha_hist_line] 96: 221 [M::ha_hist_line] 97: 226 [M::ha_hist_line] 98: 226 [M::ha_hist_line] 99: * 226 [M::ha_hist_line] 100: ** 234 [M::ha_hist_line] 101: * 221 [M::ha_hist_line] 102: *** 221 [M::ha_hist_line] 103: * 182 [M::ha_hist_line] 104: *** 222 [M::ha_hist_line] 105: ** 207 [M::ha_hist_line] 106: * 182 [M::ha_hist_line] 107: * 216 [M::ha_hist_line] 108: *** 244 [M::ha_hist_line] 109: * 194 [M::ha_hist_line] 110: **** 201 [M::ha_hist_line] 111: ***** 204 [M::ha_hist_line] 112: **** 153 [M::ha_hist_line] 113: 144 [M::ha_hist_line] 114: 164 [M::ha_hist_line] 115: 166 [M::ha_hist_line] 116: ** 184 [M::ha_hist_line] 117: **** 135 [M::ha_hist_line] 118: * 131 [M::ha_hist_line] 119: **** 146 [M::ha_hist_line] 120: ** 150 [M::ha_hist_line] 121: *** 138 [M::ha_hist_line] 122: ** 129 [M::ha_hist_line] 123: ** 129 [M::ha_hist_line] 124: **** 142 [M::ha_hist_line] 125: 133 [M::ha_hist_line] 126: ** 140 [M::ha_hist_line] 127: **** 123 [M::ha_hist_line] 128: ** 121 [M::ha_hist_line] 129: 116 [M::ha_hist_line] 130: ** 107 [M::ha_hist_line] 131: *** 116 [M::ha_hist_line] 132: * 98 [M::ha_hist_line] 133: **** 103 [M::ha_hist_line] 134: 93 [M::ha_hist_line] 135: **** 100 [M::ha_hist_line] 136: ** 94 [M::ha_hist_line] 137: **** 91 [M::ha_hist_line] 138: *** 103 [M::ha_hist_line] 139: ** 94 [M::ha_hist_line] 140: ** 73 [M::ha_hist_line] 141: ** 72 [M::ha_hist_line] 142: **** 68 [M::ha_hist_line] 143: ** 63 [M::ha_hist_line] 144: * 54 [M::ha_hist_line] 145: *** 71 [M::ha_hist_line] 146: **** 57 [M::ha_hist_line] 147: **** 66 [M::ha_hist_line] 148: * 54 [M::ha_hist_line] 149: ** 63 [M::ha_hist_line] 150: * 54 [M::ha_hist_line] 151: *** 59 [M::ha_hist_line] 152: * 36 [M::ha_hist_line] 153: *** 52 [M::ha_hist_line] 154: **** 45 [M::ha_hist_line] 155: ** 39 [M::ha_hist_line] 156: * 30 [M::ha_hist_line] 157: **** 34 [M::ha_hist_line] 158: ***** 43 [M::ha_hist_line] 159: * 42 [M::ha_hist_line] 160: ** 38 [M::ha_hist_line] 161: *** 49 [M::ha_hist_line] 162: * 30 [M::ha_hist_line] 163: *** 37 [M::ha_hist_line] 164: ** 49 [M::ha_hist_line] 165: 42 [M::ha_hist_line] 166: ** 38 [M::ha_hist_line] 167: ** 43 [M::ha_hist_line] 168: 37 [M::ha_hist_line] 169: * 37 [M::ha_hist_line] 170: ** 46 [M::ha_hist_line] 171: ** 27 [M::ha_hist_line] 172: * 30 [M::ha_hist_line] 173: ** 29 [M::ha_hist_line] 174: ** 36 [M::ha_hist_line] 175: 31 [M::ha_hist_line] 176: **** 33 [M::ha_hist_line] 177: 37 [M::ha_hist_line] 178: 36 [M::ha_hist_line] 179: * 37 [M::ha_hist_line] 180: ** 34 [M::ha_hist_line] 181: * 30 [M::ha_hist_line] 182: **** 22 [M::ha_hist_line] 183: 20 [M::ha_hist_line] 184: 20 [M::ha_hist_line] 185: * 24 [M::ha_hist_line] 186: ** 34 [M::ha_hist_line] 187: ** 27 [M::ha_hist_line] 188: * 21 [M::ha_hist_line] 189: ** 18 [M::ha_hist_line] 190: * 30 [M::ha_hist_line] 191: ** 23 [M::ha_hist_line] 192: **** 22 [M::ha_hist_line] 193: * 24 [M::ha_hist_line] 194: ** 17 [M::ha_hist_line] 195: ** 18 [M::ha_hist_line] 196: * 19 [M::ha_hist_line] 197: ** 16 [M::ha_hist_line] 198: * 20 [M::ha_hist_line] 199: * 19 [M::ha_hist_line] 200: 12 [M::ha_hist_line] 201: * 8 [M::ha_hist_line] 202: 11 [M::ha_hist_line] 203: *** 24 [M::ha_hist_line] 204: * 21 [M::ha_hist_line] 205: ** 17 [M::ha_hist_line] 206: **** 23 [M::ha_hist_line] 207: * 8 [M::ha_hist_line] 208: 10 [M::ha_hist_line] 209: 11 [M::ha_hist_line] 210: * 9 [M::ha_hist_line] 211: * 8 [M::ha_hist_line] 212: *** 13 [M::ha_hist_line] 213: * 14 [M::ha_hist_line] 214: * 12 [M::ha_hist_line] 215: 20 [M::ha_hist_line] 216: ** 12 [M::ha_hist_line] 217: 7 [M::ha_hist_line] 218: 12 [M::ha_hist_line] 219: ** 16 [M::ha_hist_line] 220: ** 18 [M::ha_hist_line] 221: 10 [M::ha_hist_line] 222: 11 [M::ha_hist_line] 223: 10 [M::ha_hist_line] 224: 10 [M::ha_hist_line] 225: 14 [M::ha_hist_line] 226: 14 [M::ha_hist_line] 227: 11 [M::ha_hist_line] 228: * 13 [M::ha_hist_line] 229: ** 12 [M::ha_hist_line] 230: * 19 [M::ha_hist_line] 231: 14 [M::ha_hist_line] 232: 14 [M::ha_hist_line] 233: 14 [M::ha_hist_line] 234: 14 [M::ha_hist_line] 235: ** 20 [M::ha_hist_line] 236: 14 [M::ha_hist_line] 237: * 8 [M::ha_hist_line] 238: ** 12 [M::ha_hist_line] 239: 6 [M::ha_hist_line] 240: 5 [M::ha_hist_line] 241: 7 [M::ha_hist_line] 242: *** 10 [M::ha_hist_line] 243: 9 [M::ha_hist_line] 244: * 11 [M::ha_hist_line] 245: 3 [M::ha_hist_line] 246: * 9 [M::ha_hist_line] 247: * 4 [M::ha_hist_line] 248: 9 [M::ha_hist_line] 249: 6 [M::ha_hist_line] 250: ** 12 [M::ha_hist_line] 251: ** 7 [M::ha_hist_line] 252: 2 [M::ha_hist_line] 253: ** 8 [M::ha_hist_line] 254: 4 [M::ha_hist_line] 255: 5 [M::ha_hist_line] 256: * 3 [M::ha_hist_line] 257: 9 [M::ha_hist_line] 258: 4 [M::ha_hist_line] 259: 3 [M::ha_hist_line] 260: 4 [M::ha_hist_line] 261: 4 [M::ha_hist_line] 262: 4 [M::ha_hist_line] 263: * 2 [M::ha_hist_line] 264: * 5 [M::ha_hist_line] 265: 4 [M::ha_hist_line] 266: 7 [M::ha_hist_line] 267: 3 [M::ha_hist_line] 268: 3 [M::ha_hist_line] 269: 5 [M::ha_hist_line] 270: 8 [M::ha_hist_line] 271: 5 [M::ha_hist_line] 272: 9 [M::ha_hist_line] 273: 6 [M::ha_hist_line] 274: * 4 [M::ha_hist_line] 275: ** 11 [M::ha_hist_line] 276: 6 [M::ha_hist_line] 277: * 2 [M::ha_hist_line] 278: ** 8 [M::ha_hist_line] 279: 4 [M::ha_hist_line] 280: 3 [M::ha_hist_line] 281: 8 [M::ha_hist_line] 282: 3 [M::ha_hist_line] 283: 3 [M::ha_hist_line] 284: 4 [M::ha_hist_line] 285: 4 [M::ha_hist_line] 286: 4 [M::ha_hist_line] 287: 3 [M::ha_hist_line] rest: ****> 297 [M::ha_analyze_count] left: count[42] = 278 [M::ha_analyze_count] right: count[89] = 251 [M::ha_pt_gen] peak_hom: 42; peak_het: -1 [M::ha_ct_shrink::16.4721.90] ==> counted 37224 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2686566 minimizers [M::ha_pt_gen::17.0392.11] ==> indexed 2633211 positions, counted 37224 distinct minimizer k-mers [M::ha_assemble::52.85113.68@16.468GB] ==> corrected reads for round 1 [M::ha_assemble] # bases: 100999180; # corrected bases: 123207; # recorrected bases: 653 [M::ha_assemble] size of buffer: 1.157GB [M::yak_count] collected 2686680 minimizers [M::ha_pt_gen::53.34313.64] ==> counted 35618 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 295 [M::ha_analyze_count] highest: count[7] = 308 [M::ha_hist_line] 1: ****> 3071 [M::ha_hist_line] 2: ****> 1048 [M::ha_hist_line] 3: ****> 680 [M::ha_hist_line] 4: ****> 431 [M::ha_hist_line] 5: ****> 337 [M::ha_hist_line] 6: **** 295 [M::ha_hist_line] 7: **** 308 [M::ha_hist_line] 8: ** 192 [M::ha_hist_line] 9: * 207 [M::ha_hist_line] 10: **** 223 [M::ha_hist_line] 11: **** 208 [M::ha_hist_line] 12: **** 196 [M::ha_hist_line] 13: ***** 242 [M::ha_hist_line] 14: * 152 [M::ha_hist_line] 15: ** 227 [M::ha_hist_line] 16: ***** 188 [M::ha_hist_line] 17: * 144 [M::ha_hist_line] 18: *** 177 [M::ha_hist_line] 19: ** 153 [M::ha_hist_line] 20: * 164 [M::ha_hist_line] 21: *** 183 [M::ha_hist_line] 22: **** 122 [M::ha_hist_line] 23: * 146 [M::ha_hist_line] 24: ** 154 [M::ha_hist_line] 25: ** 154 [M::ha_hist_line] 26: *** 150 [M::ha_hist_line] 27: ** 167 [M::ha_hist_line] 28: * 176 [M::ha_hist_line] 29: ** 174 [M::ha_hist_line] 30: ** 143 [M::ha_hist_line] 31: **** 160 [M::ha_hist_line] 32: * 169 [M::ha_hist_line] 33: ** 179 [M::ha_hist_line] 34: * 193 [M::ha_hist_line] 35: ** 252 [M::ha_hist_line] 36: *** 224 [M::ha_hist_line] 37: * 243 [M::ha_hist_line] 38: ** 277 [M::ha_hist_line] 39: **** 234 [M::ha_hist_line] 40: ** 266 [M::ha_hist_line] 41: ** 192 [M::ha_hist_line] 42: *** 274 [M::ha_hist_line] 43: * 232 [M::ha_hist_line] 44: ** 246 [M::ha_hist_line] 45: * 224 [M::ha_hist_line] 46: * 205 [M::ha_hist_line] 47: ** 227 [M::ha_hist_line] 48: ** 215 [M::ha_hist_line] 49: *** 225 [M::ha_hist_line] 50: * 220 [M::ha_hist_line] 51: *** 238 [M::ha_hist_line] 52: **** 222 [M::ha_hist_line] 53: ***** 286 [M::ha_hist_line] 54: * 189 [M::ha_hist_line] 55: ***** 230 [M::ha_hist_line] 56: ** 217 [M::ha_hist_line] 57: * 205 [M::ha_hist_line] 58: * 189 [M::ha_hist_line] 59: *** 230 [M::ha_hist_line] 60: ** 264 [M::ha_hist_line] 61: ** 229 [M::ha_hist_line] 62: ** 215 [M::ha_hist_line] 63: * 231 [M::ha_hist_line] 64: ** 246 [M::ha_hist_line] 65: **** 223 [M::ha_hist_line] 66: **** 208 [M::ha_hist_line] 67: **** 197 [M::ha_hist_line] 68: * 224 [M::ha_hist_line] 69: ** 216 [M::ha_hist_line] 70: 219 [M::ha_hist_line] 71: 220 [M::ha_hist_line] 72: **** 222 [M::ha_hist_line] 73: ***** 250 [M::ha_hist_line] 74: * 224 [M::ha_hist_line] 75: * 243 [M::ha_hist_line] 76: ***** 255 [M::ha_hist_line] 77: *** 269 [M::ha_hist_line] 78: ** 253 [M::ha_hist_line] 79: * 251 [M::ha_hist_line] 80: ** 254 [M::ha_hist_line] 81: ***** 237 [M::ha_hist_line] 82: **** 196 [M::ha_hist_line] 83: **** 221 [M::ha_hist_line] 84: * 211 [M::ha_hist_line] 85: **** 199 [M::ha_hist_line] 86: 187 [M::ha_hist_line] 87: **** 160 [M::ha_hist_line] 88: * 169 [M::ha_hist_line] 89: *** 212 [M::ha_hist_line] 90: **** 222 [M::ha_hist_line] 91: * 201 [M::ha_hist_line] 92: **** 223 [M::ha_hist_line] 93: ***** 250 [M::ha_hist_line] 94: ** 227 [M::ha_hist_line] 95: ***** 269 [M::ha_hist_line] 96: **** 221 [M::ha_hist_line] 97: ** 254 [M::ha_hist_line] 98: **** 184 [M::ha_hist_line] 99: **** 196 [M::ha_hist_line] 100: * 232 [M::ha_hist_line] 101: *** 220 [M::ha_hist_line] 102: * 199 [M::ha_hist_line] 103: ** 232 [M::ha_hist_line] 104: 225 [M::ha_hist_line] 105: *** 205 [M::ha_hist_line] 106: ** 202 [M::ha_hist_line] 107: ** 204 [M::ha_hist_line] 108: * 187 [M::ha_hist_line] 109: * 205 [M::ha_hist_line] 110: **** 210 [M::ha_hist_line] 111: *** 249 [M::ha_hist_line] 112: **** 210 [M::ha_hist_line] 113: ** 155 [M::ha_hist_line] 114: ** 142 [M::ha_hist_line] 115: * 158 [M::ha_hist_line] 116: *** 189 [M::ha_hist_line] 117: * 157 [M::ha_hist_line] 118: **** 137 [M::ha_hist_line] 119: * 157 [M::ha_hist_line] 120: ** 141 [M::ha_hist_line] 121: * 163 [M::ha_hist_line] 122: ** 111 [M::ha_hist_line] 123: * 158 [M::ha_hist_line] 124: ** 130 [M::ha_hist_line] 125: * 114 [M::ha_hist_line] 126: ** 118 [M::ha_hist_line] 127: ** 155 [M::ha_hist_line] 128: ***** 151 [M::ha_hist_line] 129: ***** 163 [M::ha_hist_line] 130: ** 128 [M::ha_hist_line] 131: * 103 [M::ha_hist_line] 132: * 109 [M::ha_hist_line] 133: **** 110 [M::ha_hist_line] 134: * 107 [M::ha_hist_line] 135: * 89 [M::ha_hist_line] 136: *** 96 [M::ha_hist_line] 137: * 90 [M::ha_hist_line] 138: ** 110 [M::ha_hist_line] 139: * 82 [M::ha_hist_line] 140: * 101 [M::ha_hist_line] 141: **** 106 [M::ha_hist_line] 142: * 96 [M::ha_hist_line] 143: * 71 [M::ha_hist_line] 144: **** 61 [M::ha_hist_line] 145: **** 74 [M::ha_hist_line] 146: * 59 [M::ha_hist_line] 147: ** 67 [M::ha_hist_line] 148: **** 62 [M::ha_hist_line] 149: * 58 [M::ha_hist_line] 150: ** 79 [M::ha_hist_line] 151: * 60 [M::ha_hist_line] 152: ** 43 [M::ha_hist_line] 153: **** 50 [M::ha_hist_line] 154: * 53 [M::ha_hist_line] 155: ** 50 [M::ha_hist_line] 156: ** 42 [M::ha_hist_line] 157: **** 37 [M::ha_hist_line] 158: **** 36 [M::ha_hist_line] 159: ** 44 [M::ha_hist_line] 160: ** 44 [M::ha_hist_line] 161: ** 44 [M::ha_hist_line] 162: * 45 [M::ha_hist_line] 163: * 33 [M::ha_hist_line] 164: **** 37 [M::ha_hist_line] 165: ** 31 [M::ha_hist_line] 166: * 33 [M::ha_hist_line] 167: * 46 [M::ha_hist_line] 168: *** 53 [M::ha_hist_line] 169: 46 [M::ha_hist_line] 170: 46 [M::ha_hist_line] 171: * 35 [M::ha_hist_line] 172: ** 32 [M::ha_hist_line] 173: * 33 [M::ha_hist_line] 174: ** 30 [M::ha_hist_line] 175: * 29 [M::ha_hist_line] 176: **** 38 [M::ha_hist_line] 177: * 29 [M::ha_hist_line] 178: * 34 [M::ha_hist_line] 179: ** 30 [M::ha_hist_line] 180: * 35 [M::ha_hist_line] 181: * 46 [M::ha_hist_line] 182: ** 31 [M::ha_hist_line] 183: * 34 [M::ha_hist_line] 184: ** 27 [M::ha_hist_line] 185: 23 [M::ha_hist_line] 186: * 14 [M::ha_hist_line] 187: ** 30 [M::ha_hist_line] 188: ***** 28 [M::ha_hist_line] 189: ** 31 [M::ha_hist_line] 190: ** 30 [M::ha_hist_line] 191: * 23 [M::ha_hist_line] 192: *** 28 [M::ha_hist_line] 193: ** 20 [M::ha_hist_line] 194: ** 18 [M::ha_hist_line] 195: **** 24 [M::ha_hist_line] 196: * 14 [M::ha_hist_line] 197: ** 18 [M::ha_hist_line] 198: ** 17 [M::ha_hist_line] 199: **** 36 [M::ha_hist_line] 200: *** 12 [M::ha_hist_line] 201: 14 [M::ha_hist_line] 202: 15 [M::ha_hist_line] 203: 14 [M::ha_hist_line] 204: 12 [M::ha_hist_line] 205: **** 22 [M::ha_hist_line] 206: 23 [M::ha_hist_line] 207: * 21 [M::ha_hist_line] 208: *** 11 [M::ha_hist_line] 209: 22 [M::ha_hist_line] 210: * 14 [M::ha_hist_line] 211: **** 19 [M::ha_hist_line] 212: * 8 [M::ha_hist_line] 213: * 9 [M::ha_hist_line] 214: *** 11 [M::ha_hist_line] 215: 10 [M::ha_hist_line] 216: 16 [M::ha_hist_line] 217: 16 [M::ha_hist_line] 218: * 8 [M::ha_hist_line] 219: ** 17 [M::ha_hist_line] 220: * 10 [M::ha_hist_line] 221: * 15 [M::ha_hist_line] 222: ** 19 [M::ha_hist_line] 223: 12 [M::ha_hist_line] 224: 12 [M::ha_hist_line] 225: 5 [M::ha_hist_line] 226: **** 17 [M::ha_hist_line] 227: 13 [M::ha_hist_line] 228: 11 [M::ha_hist_line] 229: * 15 [M::ha_hist_line] 230: * 14 [M::ha_hist_line] 231: * 5 [M::ha_hist_line] 232: 16 [M::ha_hist_line] 233: ** 11 [M::ha_hist_line] 234: ** 8 [M::ha_hist_line] 235: 9 [M::ha_hist_line] 236: ** 20 [M::ha_hist_line] 237: 11 [M::ha_hist_line] 238: **** 15 [M::ha_hist_line] 239: 16 [M::ha_hist_line] 240: ** 17 [M::ha_hist_line] 241: * 15 [M::ha_hist_line] 242: 6 [M::ha_hist_line] 243: 7 [M::ha_hist_line] 244: ** 12 [M::ha_hist_line] 245: 7 [M::ha_hist_line] 246: 6 [M::ha_hist_line] 247: * 8 [M::ha_hist_line] 248: ** 12 [M::ha_hist_line] 249: 8 [M::ha_hist_line] 250: 6 [M::ha_hist_line] 251: 9 [M::ha_hist_line] 252: 7 [M::ha_hist_line] 253: ** 11 [M::ha_hist_line] 254: 5 [M::ha_hist_line] 255: 7 [M::ha_hist_line] 256: 3 [M::ha_hist_line] 257: 6 [M::ha_hist_line] 258: 6 [M::ha_hist_line] 259: 3 [M::ha_hist_line] 260: 5 [M::ha_hist_line] 261: 2 [M::ha_hist_line] 262: 3 [M::ha_hist_line] 263: 2 [M::ha_hist_line] 264: 3 [M::ha_hist_line] 265: 2 [M::ha_hist_line] 266: 3 [M::ha_hist_line] 267: * 3 [M::ha_hist_line] 268: 7 [M::ha_hist_line] 269: 6 [M::ha_hist_line] 270: 5 [M::ha_hist_line] 271: 6 [M::ha_hist_line] 272: 5 [M::ha_hist_line] 273: 2 [M::ha_hist_line] 274: 3 [M::ha_hist_line] 275: 5 [M::ha_hist_line] 276: * 6 [M::ha_hist_line] 277: 9 [M::ha_hist_line] 278: * 9 [M::ha_hist_line] 279: 7 [M::ha_hist_line] 280: 7 [M::ha_hist_line] 281: * 6 [M::ha_hist_line] 282: 9 [M::ha_hist_line] 283: * 9 [M::ha_hist_line] 284: 7 [M::ha_hist_line] 285: 5 [M::ha_hist_line] 286: 5 [M::ha_hist_line] rest: **> 314 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 50; peak_het: 7 [M::ha_ct_shrink::53.36513.64] ==> counted 32547 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2686680 minimizers [M::ha_pt_gen::53.81013.61] ==> indexed 2683609 positions, counted 32547 distinct minimizer k-mers [M::ha_assemble::83.46416.05@16.468GB] ==> corrected reads for round 2 [M::ha_assemble] # bases: 101006457; # corrected bases: 7201; # recorrected bases: 184 [M::ha_assemble] size of buffer: 0.958GB [M::yak_count] collected 2686842 minimizers [M::ha_pt_gen::83.92516.01] ==> counted 34642 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 298 [M::ha_analyze_count] highest: count[7] = 304 [M::ha_hist_line] 1: ****> 2323 [M::ha_hist_line] 2: ****> 858 [M::ha_hist_line] 3: ****> 659 [M::ha_hist_line] 4: ****> 432 [M::ha_hist_line] 5: ****> 327 [M::ha_hist_line] 6: ** 298 [M::ha_hist_line] 7: **** 304 [M::ha_hist_line] 8: *** 198 [M::ha_hist_line] 9: **** 206 [M::ha_hist_line] 10: *** 223 [M::ha_hist_line] 11: **** 206 [M::ha_hist_line] 12: **** 195 [M::ha_hist_line] 13: ** 238 [M::ha_hist_line] 14: * 156 [M::ha_hist_line] 15: *** 221 [M::ha_hist_line] 16: ** 189 [M::ha_hist_line] 17: * 143 [M::ha_hist_line] 18: *** 180 [M::ha_hist_line] 19: * 150 [M::ha_hist_line] 20: ** 165 [M::ha_hist_line] 21: ***** 180 [M::ha_hist_line] 22: ** 127 [M::ha_hist_line] 23: ** 140 [M::ha_hist_line] 24: * 155 [M::ha_hist_line] 25: **** 157 [M::ha_hist_line] 26: **** 147 [M::ha_hist_line] 27: **** 171 [M::ha_hist_line] 28: ** 163 [M::ha_hist_line] 29: **** 181 [M::ha_hist_line] 30: **** 146 [M::ha_hist_line] 31: * 161 [M::ha_hist_line] 32: ** 164 [M::ha_hist_line] 33: *** 178 [M::ha_hist_line] 34: **** 196 [M::ha_hist_line] 35: ** 236 [M::ha_hist_line] 36: * 241 [M::ha_hist_line] 37: **** 244 [M::ha_hist_line] 38: *** 272 [M::ha_hist_line] 39: ** 237 [M::ha_hist_line] 40: ** 262 [M::ha_hist_line] 41: * 191 [M::ha_hist_line] 42: ** 275 [M::ha_hist_line] 43: **** 230 [M::ha_hist_line] 44: *** 245 [M::ha_hist_line] 45: * 228 [M::ha_hist_line] 46: **** 208 [M::ha_hist_line] 47: ** 225 [M::ha_hist_line] 48: ** 213 [M::ha_hist_line] 49: ** 225 [M::ha_hist_line] 50: **** 219 [M::ha_hist_line] 51: ***** 240 [M::ha_hist_line] 52: **** 219 [M::ha_hist_line] 53: *** 277 [M::ha_hist_line] 54: * 198 [M::ha_hist_line] 55: **** 232 [M::ha_hist_line] 56: ** 214 [M::ha_hist_line] 57: ** 200 [M::ha_hist_line] 58: ** 190 [M::ha_hist_line] 59: **** 232 [M::ha_hist_line] 60: ** 261 [M::ha_hist_line] 61: **** 232 [M::ha_hist_line] 62: * 217 [M::ha_hist_line] 63: ***** 227 [M::ha_hist_line] 64: ***** 246 [M::ha_hist_line] 65: ** 226 [M::ha_hist_line] 66: * 209 [M::ha_hist_line] 67: **** 196 [M::ha_hist_line] 68: * 223 [M::ha_hist_line] 69: ** 214 [M::ha_hist_line] 70: ** 213 [M::ha_hist_line] 71: *** 227 [M::ha_hist_line] 72: ** 226 [M::ha_hist_line] 73: ** 250 [M::ha_hist_line] 74: ** 213 [M::ha_hist_line] 75: * 247 [M::ha_hist_line] 76: **** 255 [M::ha_hist_line] 77: *** 266 [M::ha_hist_line] 78: **** 256 [M::ha_hist_line] 79: ** 248 [M::ha_hist_line] 80: **** 255 [M::ha_hist_line] 81: ***** 240 [M::ha_hist_line] 82: * 193 [M::ha_hist_line] 83: ***** 228 [M::ha_hist_line] 84: **** 206 [M::ha_hist_line] 85: * 193 [M::ha_hist_line] 86: ** 188 [M::ha_hist_line] 87: 167 [M::ha_hist_line] 88: 168 [M::ha_hist_line] 89: * 205 [M::ha_hist_line] 90: **** 231 [M::ha_hist_line] 91: * 203 [M::ha_hist_line] 92: * 221 [M::ha_hist_line] 93: ** 249 [M::ha_hist_line] 94: **** 220 [M::ha_hist_line] 95: ***** 271 [M::ha_hist_line] 96: ** 225 [M::ha_hist_line] 97: **** 254 [M::ha_hist_line] 98: **** 183 [M::ha_hist_line] 99: **** 194 [M::ha_hist_line] 100: **** 231 [M::ha_hist_line] 101: * 221 [M::ha_hist_line] 102: **** 202 [M::ha_hist_line] 103: **** 232 [M::ha_hist_line] 104: * 217 [M::ha_hist_line] 105: ** 211 [M::ha_hist_line] 106: 203 [M::ha_hist_line] 107: **** 207 [M::ha_hist_line] 108: * 184 [M::ha_hist_line] 109: **** 208 [M::ha_hist_line] 110: ***** 209 [M::ha_hist_line] 111: ** 250 [M::ha_hist_line] 112: **** 208 [M::ha_hist_line] 113: **** 157 [M::ha_hist_line] 114: * 137 [M::ha_hist_line] 115: *** 155 [M::ha_hist_line] 116: *** 191 [M::ha_hist_line] 117: * 160 [M::ha_hist_line] 118: * 138 [M::ha_hist_line] 119: ** 157 [M::ha_hist_line] 120: * 131 [M::ha_hist_line] 121: *** 167 [M::ha_hist_line] 122: * 112 [M::ha_hist_line] 123: **** 157 [M::ha_hist_line] 124: **** 135 [M::ha_hist_line] 125: * 119 [M::ha_hist_line] 126: ** 115 [M::ha_hist_line] 127: ** 151 [M::ha_hist_line] 128: ** 153 [M::ha_hist_line] 129: ***** 167 [M::ha_hist_line] 130: *** 132 [M::ha_hist_line] 131: * 101 [M::ha_hist_line] 132: **** 108 [M::ha_hist_line] 133: *** 114 [M::ha_hist_line] 134: **** 108 [M::ha_hist_line] 135: ** 91 [M::ha_hist_line] 136: ** 92 [M::ha_hist_line] 137: * 93 [M::ha_hist_line] 138: ** 104 [M::ha_hist_line] 139: * 88 [M::ha_hist_line] 140: ** 103 [M::ha_hist_line] 141: *** 105 [M::ha_hist_line] 142: ***** 93 [M::ha_hist_line] 143: **** 73 [M::ha_hist_line] 144: **** 61 [M::ha_hist_line] 145: **** 73 [M::ha_hist_line] 146: * 58 [M::ha_hist_line] 147: ** 67 [M::ha_hist_line] 148: **** 62 [M::ha_hist_line] 149: ** 55 [M::ha_hist_line] 150: ** 80 [M::ha_hist_line] 151: * 58 [M::ha_hist_line] 152: ** 48 [M::ha_hist_line] 153: **** 49 [M::ha_hist_line] 154: * 53 [M::ha_hist_line] 155: **** 50 [M::ha_hist_line] 156: 41 [M::ha_hist_line] 157: 39 [M::ha_hist_line] 158: **** 36 [M::ha_hist_line] 159: ** 44 [M::ha_hist_line] 160: 45 [M::ha_hist_line] 161: 45 [M::ha_hist_line] 162: **** 45 [M::ha_hist_line] 163: 33 [M::ha_hist_line] 164: **** 38 [M::ha_hist_line] 165: ** 31 [M::ha_hist_line] 166: * 33 [M::ha_hist_line] 167: ***** 46 [M::ha_hist_line] 168: * 52 [M::ha_hist_line] 169: **** 42 [M::ha_hist_line] 170: * 45 [M::ha_hist_line] 171: **** 36 [M::ha_hist_line] 172: **** 35 [M::ha_hist_line] 173: ** 34 [M::ha_hist_line] 174: 26 [M::ha_hist_line] 175: * 28 [M::ha_hist_line] 176: ** 42 [M::ha_hist_line] 177: ** 29 [M::ha_hist_line] 178: *** 34 [M::ha_hist_line] 179: ** 29 [M::ha_hist_line] 180: **** 35 [M::ha_hist_line] 181: **** 48 [M::ha_hist_line] 182: 32 [M::ha_hist_line] 183: 32 [M::ha_hist_line] 184: * 27 [M::ha_hist_line] 185: **** 23 [M::ha_hist_line] 186: * 15 [M::ha_hist_line] 187: * 28 [M::ha_hist_line] 188: ** 29 [M::ha_hist_line] 189: *** 32 [M::ha_hist_line] 190: * 28 [M::ha_hist_line] 191: **** 25 [M::ha_hist_line] 192: * 26 [M::ha_hist_line] 193: ** 18 [M::ha_hist_line] 194: **** 23 [M::ha_hist_line] 195: ** 20 [M::ha_hist_line] 196: 14 [M::ha_hist_line] 197: ** 19 [M::ha_hist_line] 198: * 16 [M::ha_hist_line] 199: ***** 40 [M::ha_hist_line] 200: 12 [M::ha_hist_line] 201: 13 [M::ha_hist_line] 202: 16 [M::ha_hist_line] 203: 14 [M::ha_hist_line] 204: 13 [M::ha_hist_line] 205: * 21 [M::ha_hist_line] 206: **** 23 [M::ha_hist_line] 207: * 21 [M::ha_hist_line] 208: 12 [M::ha_hist_line] 209: **** 23 [M::ha_hist_line] 210: 13 [M::ha_hist_line] 211: ** 19 [M::ha_hist_line] 212: * 9 [M::ha_hist_line] 213: 7 [M::ha_hist_line] 214: ** 12 [M::ha_hist_line] 215: * 9 [M::ha_hist_line] 216: 15 [M::ha_hist_line] 217: 15 [M::ha_hist_line] 218: 7 [M::ha_hist_line] 219: **** 17 [M::ha_hist_line] 220: 12 [M::ha_hist_line] 221: * 16 [M::ha_hist_line] 222: ** 19 [M::ha_hist_line] 223: 12 [M::ha_hist_line] 224: 11 [M::ha_hist_line] 225: * 5 [M::ha_hist_line] 226: 14 [M::ha_hist_line] 227: ** 15 [M::ha_hist_line] 228: 9 [M::ha_hist_line] 229: ** 18 [M::ha_hist_line] 230: * 14 [M::ha_hist_line] 231: 5 [M::ha_hist_line] 232: 13 [M::ha_hist_line] 233: 11 [M::ha_hist_line] 234: *** 12 [M::ha_hist_line] 235: 9 [M::ha_hist_line] 236: * 20 [M::ha_hist_line] 237: ** 11 [M::ha_hist_line] 238: * 14 [M::ha_hist_line] 239: ** 17 [M::ha_hist_line] 240: ** 17 [M::ha_hist_line] 241: 14 [M::ha_hist_line] 242: 5 [M::ha_hist_line] 243: 8 [M::ha_hist_line] 244: ** 13 [M::ha_hist_line] 245: 7 [M::ha_hist_line] 246: 6 [M::ha_hist_line] 247: 7 [M::ha_hist_line] 248: ** 11 [M::ha_hist_line] 249: * 8 [M::ha_hist_line] 250: 5 [M::ha_hist_line] 251: *** 11 [M::ha_hist_line] 252: 8 [M::ha_hist_line] 253: * 11 [M::ha_hist_line] 254: 4 [M::ha_hist_line] 255: * 6 [M::ha_hist_line] 256: 4 [M::ha_hist_line] 257: 6 [M::ha_hist_line] 258: 7 [M::ha_hist_line] 259: * 3 [M::ha_hist_line] 260: * 5 [M::ha_hist_line] 261: 2 [M::ha_hist_line] 262: 3 [M::ha_hist_line] 263: 2 [M::ha_hist_line] 264: 3 [M::ha_hist_line] 265: 2 [M::ha_hist_line] 266: 3 [M::ha_hist_line] 267: 3 [M::ha_hist_line] 268: 7 [M::ha_hist_line] 269: 6 [M::ha_hist_line] 270: 4 [M::ha_hist_line] 271: 6 [M::ha_hist_line] 272: 6 [M::ha_hist_line] 273: 2 [M::ha_hist_line] 274: * 3 [M::ha_hist_line] 275: 6 [M::ha_hist_line] 276: 4 [M::ha_hist_line] 277: 8 [M::ha_hist_line] 278: * 9 [M::ha_hist_line] 279: 6 [M::ha_hist_line] 280: ** 8 [M::ha_hist_line] 281: 8 [M::ha_hist_line] 282: 9 [M::ha_hist_line] 283: 9 [M::ha_hist_line] 284: * 3 [M::ha_hist_line] 285: * 8 [M::ha_hist_line] 286: 5 [M::ha_hist_line] rest: **> 315 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 50; peak_het: 7 [M::ha_ct_shrink::83.94416.01] ==> counted 32319 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2686842 minimizers [M::ha_pt_gen::84.46815.96] ==> indexed 2684519 positions, counted 32319 distinct minimizer k-mers [M::ha_assemble::115.96816.87@16.468GB] ==> corrected reads for round 3 [M::ha_assemble] # bases: 101009728; # corrected bases: 1129; # recorrected bases: 83 [M::ha_assemble] size of buffer: 0.941GB [M::yak_count] collected 2686889 minimizers [M::ha_pt_gen::116.37916.84] ==> counted 34554 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[6] = 298 [M::ha_analyze_count] highest: count[7] = 304 [M::ha_hist_line] 1: ****> 2266 [M::ha_hist_line] 2: ****> 836 [M::ha_hist_line] 3: ****> 657 [M::ha_hist_line] 4: ****> 428 [M::ha_hist_line] 5: ****> 329 [M::ha_hist_line] 6: ** 298 [M::ha_hist_line] 7: **** 304 [M::ha_hist_line] 8: *** 197 [M::ha_hist_line] 9: * 205 [M::ha_hist_line] 10: *** 222 [M::ha_hist_line] 11: **** 206 [M::ha_hist_line] 12: **** 194 [M::ha_hist_line] 13: ** 237 [M::ha_hist_line] 14: * 156 [M::ha_hist_line] 15: *** 221 [M::ha_hist_line] 16: ** 189 [M::ha_hist_line] 17: * 143 [M::ha_hist_line] 18: ***** 179 [M::ha_hist_line] 19: ** 151 [M::ha_hist_line] 20: ** 165 [M::ha_hist_line] 21: ***** 180 [M::ha_hist_line] 22: ** 127 [M::ha_hist_line] 23: ** 140 [M::ha_hist_line] 24: * 155 [M::ha_hist_line] 25: **** 157 [M::ha_hist_line] 26: **** 147 [M::ha_hist_line] 27: **** 171 [M::ha_hist_line] 28: ** 163 [M::ha_hist_line] 29: **** 181 [M::ha_hist_line] 30: **** 146 [M::ha_hist_line] 31: * 161 [M::ha_hist_line] 32: ** 164 [M::ha_hist_line] 33: *** 178 [M::ha_hist_line] 34: * 193 [M::ha_hist_line] 35: **** 242 [M::ha_hist_line] 36: ** 238 [M::ha_hist_line] 37: **** 243 [M::ha_hist_line] 38: ** 273 [M::ha_hist_line] 39: ** 236 [M::ha_hist_line] 40: ** 262 [M::ha_hist_line] 41: * 192 [M::ha_hist_line] 42: ***** 276 [M::ha_hist_line] 43: * 229 [M::ha_hist_line] 44: *** 245 [M::ha_hist_line] 45: * 228 [M::ha_hist_line] 46: * 209 [M::ha_hist_line] 47: ** 224 [M::ha_hist_line] 48: ** 213 [M::ha_hist_line] 49: ** 225 [M::ha_hist_line] 50: **** 219 [M::ha_hist_line] 51: *** 240 [M::ha_hist_line] 52: **** 220 [M::ha_hist_line] 53: *** 276 [M::ha_hist_line] 54: * 198 [M::ha_hist_line] 55: ***** 233 [M::ha_hist_line] 56: ** 213 [M::ha_hist_line] 57: * 197 [M::ha_hist_line] 58: * 193 [M::ha_hist_line] 59: **** 230 [M::ha_hist_line] 60: ** 261 [M::ha_hist_line] 61: **** 231 [M::ha_hist_line] 62: **** 219 [M::ha_hist_line] 63: ***** 227 [M::ha_hist_line] 64: **** 244 [M::ha_hist_line] 65: ** 226 [M::ha_hist_line] 66: * 210 [M::ha_hist_line] 67: **** 196 [M::ha_hist_line] 68: ***** 223 [M::ha_hist_line] 69: ** 214 [M::ha_hist_line] 70: ** 213 [M::ha_hist_line] 71: 228 [M::ha_hist_line] 72: 227 [M::ha_hist_line] 73: ** 250 [M::ha_hist_line] 74: ** 213 [M::ha_hist_line] 75: * 247 [M::ha_hist_line] 76: *** 252 [M::ha_hist_line] 77: **** 269 [M::ha_hist_line] 78: **** 256 [M::ha_hist_line] 79: *** 247 [M::ha_hist_line] 80: **** 254 [M::ha_hist_line] 81: ** 236 [M::ha_hist_line] 82: **** 195 [M::ha_hist_line] 83: **** 231 [M::ha_hist_line] 84: **** 206 [M::ha_hist_line] 85: **** 194 [M::ha_hist_line] 86: ** 187 [M::ha_hist_line] 87: * 166 [M::ha_hist_line] 88: * 167 [M::ha_hist_line] 89: **** 206 [M::ha_hist_line] 90: **** 231 [M::ha_hist_line] 91: ***** 203 [M::ha_hist_line] 92: **** 220 [M::ha_hist_line] 93: ***** 247 [M::ha_hist_line] 94: * 222 [M::ha_hist_line] 95: *** 270 [M::ha_hist_line] 96: ** 224 [M::ha_hist_line] 97: * 252 [M::ha_hist_line] 98: * 184 [M::ha_hist_line] 99: *** 193 [M::ha_hist_line] 100: **** 231 [M::ha_hist_line] 101: **** 219 [M::ha_hist_line] 102: * 204 [M::ha_hist_line] 103: **** 232 [M::ha_hist_line] 104: **** 218 [M::ha_hist_line] 105: *** 210 [M::ha_hist_line] 106: **** 207 [M::ha_hist_line] 107: * 211 [M::ha_hist_line] 108: **** 181 [M::ha_hist_line] 109: **** 208 [M::ha_hist_line] 110: * 211 [M::ha_hist_line] 111: ** 249 [M::ha_hist_line] 112: ***** 210 [M::ha_hist_line] 113: **** 157 [M::ha_hist_line] 114: * 137 [M::ha_hist_line] 115: * 154 [M::ha_hist_line] 116: ***** 191 [M::ha_hist_line] 117: ***** 161 [M::ha_hist_line] 118: * 137 [M::ha_hist_line] 119: ***** 156 [M::ha_hist_line] 120: **** 134 [M::ha_hist_line] 121: ** 165 [M::ha_hist_line] 122: **** 110 [M::ha_hist_line] 123: **** 158 [M::ha_hist_line] 124: **** 133 [M::ha_hist_line] 125: * 118 [M::ha_hist_line] 126: * 113 [M::ha_hist_line] 127: ***** 149 [M::ha_hist_line] 128: **** 159 [M::ha_hist_line] 129: **** 169 [M::ha_hist_line] 130: *** 132 [M::ha_hist_line] 131: * 101 [M::ha_hist_line] 132: **** 108 [M::ha_hist_line] 133: ** 114 [M::ha_hist_line] 134: 107 [M::ha_hist_line] 135: ** 92 [M::ha_hist_line] 136: ** 91 [M::ha_hist_line] 137: * 93 [M::ha_hist_line] 138: ***** 105 [M::ha_hist_line] 139: * 87 [M::ha_hist_line] 140: ** 104 [M::ha_hist_line] 141: ** 103 [M::ha_hist_line] 142: *** 95 [M::ha_hist_line] 143: **** 73 [M::ha_hist_line] 144: **** 61 [M::ha_hist_line] 145: **** 73 [M::ha_hist_line] 146: * 58 [M::ha_hist_line] 147: ** 67 [M::ha_hist_line] 148: **** 62 [M::ha_hist_line] 149: ** 55 [M::ha_hist_line] 150: ** 80 [M::ha_hist_line] 151: * 58 [M::ha_hist_line] 152: * 47 [M::ha_hist_line] 153: **** 49 [M::ha_hist_line] 154: *** 51 [M::ha_hist_line] 155: * 51 [M::ha_hist_line] 156: ** 42 [M::ha_hist_line] 157: * 39 [M::ha_hist_line] 158: **** 35 [M::ha_hist_line] 159: ** 44 [M::ha_hist_line] 160: 45 [M::ha_hist_line] 161: 45 [M::ha_hist_line] 162: **** 47 [M::ha_hist_line] 163: 33 [M::ha_hist_line] 164: **** 37 [M::ha_hist_line] 165: 32 [M::ha_hist_line] 166: 33 [M::ha_hist_line] 167: * 46 [M::ha_hist_line] 168: *** 52 [M::ha_hist_line] 169: ** 42 [M::ha_hist_line] 170: * 45 [M::ha_hist_line] 171: **** 35 [M::ha_hist_line] 172: **** 36 [M::ha_hist_line] 173: * 34 [M::ha_hist_line] 174: 26 [M::ha_hist_line] 175: 28 [M::ha_hist_line] 176: ** 42 [M::ha_hist_line] 177: ** 29 [M::ha_hist_line] 178: * 34 [M::ha_hist_line] 179: ** 29 [M::ha_hist_line] 180: **** 35 [M::ha_hist_line] 181: **** 48 [M::ha_hist_line] 182: * 32 [M::ha_hist_line] 183: *** 32 [M::ha_hist_line] 184: **** 25 [M::ha_hist_line] 185: **** 25 [M::ha_hist_line] 186: * 15 [M::ha_hist_line] 187: * 28 [M::ha_hist_line] 188: ** 29 [M::ha_hist_line] 189: *** 32 [M::ha_hist_line] 190: * 28 [M::ha_hist_line] 191: **** 25 [M::ha_hist_line] 192: * 26 [M::ha_hist_line] 193: ** 18 [M::ha_hist_line] 194: **** 23 [M::ha_hist_line] 195: ** 20 [M::ha_hist_line] 196: 14 [M::ha_hist_line] 197: ** 19 [M::ha_hist_line] 198: * 16 [M::ha_hist_line] 199: ***** 40 [M::ha_hist_line] 200: 12 [M::ha_hist_line] 201: 13 [M::ha_hist_line] 202: ** 18 [M::ha_hist_line] 203: * 14 [M::ha_hist_line] 204: * 11 [M::ha_hist_line] 205: 21 [M::ha_hist_line] 206: **** 23 [M::ha_hist_line] 207: * 21 [M::ha_hist_line] 208: 12 [M::ha_hist_line] 209: **** 23 [M::ha_hist_line] 210: 13 [M::ha_hist_line] 211: ** 19 [M::ha_hist_line] 212: * 9 [M::ha_hist_line] 213: 7 [M::ha_hist_line] 214: ** 12 [M::ha_hist_line] 215: * 9 [M::ha_hist_line] 216: *** 15 [M::ha_hist_line] 217: * 15 [M::ha_hist_line] 218: 7 [M::ha_hist_line] 219: **** 17 [M::ha_hist_line] 220: *** 13 [M::ha_hist_line] 221: 15 [M::ha_hist_line] 222: ** 19 [M::ha_hist_line] 223: 12 [M::ha_hist_line] 224: 11 [M::ha_hist_line] 225: 5 [M::ha_hist_line] 226: ** 14 [M::ha_hist_line] 227: 15 [M::ha_hist_line] 228: * 9 [M::ha_hist_line] 229: *** 16 [M::ha_hist_line] 230: * 16 [M::ha_hist_line] 231: 5 [M::ha_hist_line] 232: 12 [M::ha_hist_line] 233: 12 [M::ha_hist_line] 234: *** 12 [M::ha_hist_line] 235: 9 [M::ha_hist_line] 236: * 20 [M::ha_hist_line] 237: ** 11 [M::ha_hist_line] 238: * 14 [M::ha_hist_line] 239: * 16 [M::ha_hist_line] 240: ** 18 [M::ha_hist_line] 241: * 14 [M::ha_hist_line] 242: 5 [M::ha_hist_line] 243: * 8 [M::ha_hist_line] 244: ** 13 [M::ha_hist_line] 245: 7 [M::ha_hist_line] 246: 6 [M::ha_hist_line] 247: 7 [M::ha_hist_line] 248: ** 11 [M::ha_hist_line] 249: * 8 [M::ha_hist_line] 250: 5 [M::ha_hist_line] 251: ** 11 [M::ha_hist_line] 252: * 8 [M::ha_hist_line] 253: *** 11 [M::ha_hist_line] 254: 4 [M::ha_hist_line] 255: 6 [M::ha_hist_line] 256: 4 [M::ha_hist_line] 257: 6 [M::ha_hist_line] 258: 7 [M::ha_hist_line] 259: 3 [M::ha_hist_line] 260: 5 [M::ha_hist_line] 261: 2 [M::ha_hist_line] 262: 3 [M::ha_hist_line] 263: 2 [M::ha_hist_line] 264: 3 [M::ha_hist_line] 265: 2 [M::ha_hist_line] 266: 3 [M::ha_hist_line] 267: 3 [M::ha_hist_line] 268: 7 [M::ha_hist_line] 269: 6 [M::ha_hist_line] 270: 4 [M::ha_hist_line] 271: 6 [M::ha_hist_line] 272: 6 [M::ha_hist_line] 273: 2 [M::ha_hist_line] 274: 3 [M::ha_hist_line] 275: 6 [M::ha_hist_line] 276: * 4 [M::ha_hist_line] 277: 8 [M::ha_hist_line] 278: 9 [M::ha_hist_line] 279: 6 [M::ha_hist_line] 280: ** 8 [M::ha_hist_line] 281: 8 [M::ha_hist_line] 282: 9 [M::ha_hist_line] 283: 9 [M::ha_hist_line] 284: * 3 [M::ha_hist_line] 285: * 8 [M::ha_hist_line] 286: 5 [M::ha_hist_line] rest: ****> 315 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_pt_gen] peak_hom: 50; peak_het: 7 [M::ha_ct_shrink::116.39816.84] ==> counted 32288 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 2686889 minimizers [M::ha_pt_gen::116.83316.82] ==> indexed 2684623 positions, counted 32288 distinct minimizer k-mers [M::ha_assemble::127.226*17.18@16.468GB] ==> found overlaps for the final round [M::ha_print_ovlp_stat] # overlaps: 4014598 [M::ha_print_ovlp_stat] # strong overlaps: 1997279 [M::ha_print_ovlp_stat] # weak overlaps: 2017319 [M::ha_print_ovlp_stat] # exact overlaps: 3911232 [M::ha_print_ovlp_stat] # inexact overlaps: 103366 [M::ha_print_ovlp_stat] # overlaps without large indels: 4014079 [M::ha_print_ovlp_stat] # reverse overlaps: 1117045 [M::ha_opt_update_cov_min] updated max_n_chain to 50000 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: 49 [M::purge_dups] purge duplication coverage threshold: 62 [M::ug_ext_gfa::] # tips::8 Writing raw unitig GFA to disk... Writing processed unitig GFA to disk... [M::purge_dups] homozygous read coverage threshold: 49 [M::purge_dups] purge duplication coverage threshold: 62 [M::mc_solve:: # edges: 4] [M::mc_solve_core_adv::0.000] ==> Partition [M::adjust_utg_by_primary] primary contig coverage range: [41, infinity] Writing primary contig GFA to disk... Writing alternate contig GFA to disk... Inconsistency threshold for low-quality regions in BED files: 70% [M::main] Version: 0.19.8-r603 [M::main] CMD: /u/project/geschwind/leqi0001/software/hifiasm/hifiasm -o /u/project/geschwind/leqi0001/longreads/assembly_phased/GIH.92.C2.hap2 -t 32 --primary --hg-size 2m -D 1000 -N 20000 GIH.92.C2.hap2.fastq.gz [M::main] Real time: 137.101 sec; CPU: 2193.612 sec; Peak RSS: 16.468 GB