Run of program pandagma fsup, version 2023-02-29 Run started at: Thu 29 Feb 2024 06:50:18 AM PST Run ended at: Thu 29 Feb 2024 08:27:22 AM PST Parameter value consen_iden 0.30 clust_cov 0.40 consen_method align_sample annot_str_regex ([^.]+\.[^.]+)\..+ Output directory for this run: out_pandagma Report orthogroup composition statistics for the three main cluster-calculation steps Print sequence composition statistics for each annotation set == Sequence stats for protein files Class: seqs min max N50 ave annotation_name Added with align_sample: 27651 4 5401 515 405.9 arath.Col0 Added with align_sample: 82784 25 5423 493 361.4 arahy.Tifrunner Added with align_sample: 37533 4 5474 515 400.2 bauva.BV-YZ2020 Added with align_sample: 29472 49 5465 522 401.1 cajca.ICPL87119 Added with align_sample: 27311 26 5513 552 429.9 cerca.ISC453364 Added with align_sample: 29000 31 5485 536 427.3 chafa.ISC494698 Added with align_sample: 30800 14 8791 509 368.2 cicar.CDCFrontier Added with align_sample: 52798 30 5436 524 385.4 glyma.Wm82 Added with align_sample: 38256 3 5098 481 359.4 lencu.CDC_Redberry Added with align_sample: 39584 33 4350 433 296.9 lotja.MG20 Added with align_sample: 38088 40 5101 511 370.1 lupal.Amiga Added with align_sample: 49825 16 5385 487 331.4 medtr.A17_HM341 Added with align_sample: 32293 31 5431 537 415.3 phalu.G27455 Added with align_sample: 27374 30 5430 534 420.1 phavu.G19833 Added with align_sample: 44635 27 14089 456 322.4 pissa.Cameor Added with align_sample: 35789 19 5484 508 396.7 quisa.S10 Added with align_sample: 44724 17 5305 505 317.0 sento.Myeongyun Added with align_sample: 31892 42 6009 506 380.2 singl.CAF01 Added with align_sample: 39676 1 5102 491 345.0 tripr.MilvusB Added with align_sample: 34324 75 5397 485 376.5 vicfa.Hedin2 Added with align_sample: 26716 6 5687 527 390.7 vigan.Gyeongwon Added with align_sample: 30956 1 4618 490 359.6 vigra.VC1973A Added with align_sample: 31929 30 5426 534 405.1 vigun.IT97K-499-35 Avg: 37539 24 5865 506 376 all_annot_sets == Proportion of initial genes retained in the "aug_extra" set: Start End Pct_kept Annotation_name 82784 69150 83.5 arahy.Tifrunner 27651 24362 88.1 arath.Col0 37533 34223 91.2 bauva.BV-YZ2020 29472 26673 90.5 cajca.ICPL87119 27311 25686 94.1 cerca.ISC453364 29000 27449 94.7 chafa.ISC494698 30800 27126 88.1 cicar.CDCFrontier 52798 46160 87.4 glyma.Wm82 38256 34090 89.1 lencu.CDC_Redberry 39584 28614 72.3 lotja.MG20 38088 33226 87.2 lupal.Amiga 49825 37598 75.5 medtr.A17_HM341 32293 27914 86.4 phalu.G27455 27374 26103 95.4 phavu.G19833 44635 32271 72.3 pissa.Cameor 35789 32765 91.6 quisa.S10 44724 28891 64.6 sento.Myeongyun 31892 27333 85.7 singl.CAF01 39676 32724 82.5 tripr.MilvusB 34324 30354 88.4 vicfa.Hedin2 26716 23459 87.8 vigan.Gyeongwon 30956 27108 87.6 vigra.VC1973A 31929 29004 90.8 vigun.IT97K-499-35 Counts of clusters by cluster size, file 34_sup_vs_fam_consen.clust.tsv: 1 72 2 238 3 344 4 500 5 605 6 660 7 781 8 683 9 598 10 505 11 491 12 388 13 367 14 355 15 362 16 340 17 371 18 413 19 399 20 382 21 393 22 415 23 486 24 670 25 826 26 904 27 976 28 925 29 873 30 730 31 616 32 605 33 515 34 434 35 464 36 364 37 372 38 341 39 296 40 335 41 298 42 259 43 293 44 284 45 242 46 279 47 276 48 304 49 283 50 254 51 225 52 191 53 195 54 171 55 125 56 106 57 81 58 90 59 62 60 58 61 60 62 57 63 40 64 56 65 39 66 28 67 37 68 39 69 25 70 35 71 38 72 19 73 25 74 21 75 23 76 16 77 17 78 16 79 23 80 21 81 16 82 14 83 14 84 14 85 12 86 13 87 14 88 13 89 6 90 6 91 19 92 8 93 8 94 6 95 8 96 7 97 9 98 7 99 10 100 7 101 1 102 4 103 11 104 8 105 7 106 5 107 4 108 4 109 6 110 4 111 5 112 3 113 7 114 2 115 4 116 3 117 4 118 3 119 2 120 4 121 7 122 5 123 4 124 1 125 9 126 1 127 3 128 7 129 4 130 3 131 2 132 4 133 4 134 1 135 5 136 5 137 5 138 3 139 4 140 6 141 2 142 2 143 1 144 1 145 3 146 5 147 1 148 4 150 2 151 1 152 2 154 1 156 2 158 4 159 2 160 1 161 1 162 2 163 1 164 4 167 2 169 1 170 1 172 1 176 1 177 1 178 2 180 1 181 1 182 2 183 1 186 2 187 2 189 1 190 1 191 1 192 1 193 1 196 1 197 2 200 2 203 2 206 1 207 1 213 1 215 1 222 1 223 1 235 2 236 1 237 1 238 1 239 1 240 1 248 1 250 1 252 1 255 1 260 1 261 1 265 2 268 1 286 1 303 1 320 1 323 1 352 1 386 1 402 1 412 1 547 1 883 1