Run of program pandagma fsup, version 2025-05-30 Run started at: Wed Jun 11 16:01:50 CDT 2025 Run ended at: Wed Jun 11 23:42:43 CDT 2025 Parameter value consen_iden 0.20 clust_cov 0.30 TE_match_iden 0.40 annot_str_regex ([^.]+\.[^.]+)\..+ min_align_count 4 min_annots_in_align 1 evalue 1e-10 search_method hmmsearch hmmdb_path /project/legume_project/common_data/genefamilies/LegSF.fam3 prot_fam_dir cluster hmm_dir 21_hmm 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 to gene families: 29384 4 5489 520 408.1 acacr.Acra3RX Added to gene families: 32656 49 5431 541 403.3 aesev.CIAT22838 Added to gene families: 27650 4 5401 515 405.9 arath.Col0 Added to gene families: 37510 4 5474 515 400.3 bauva.BV-YZ2020 Added to gene families: 27288 26 5513 552 429.8 cerca.ISC453364 Added to gene families: 29074 31 5485 536 426.8 chafa.ISC494698 Added to gene families: 52872 30 5436 524 385.2 glyma.Wm82 Added to gene families: 50444 16 5385 485 329.1 medtr.A17_HM341 Added to gene families: 37229 24 5535 466 296.1 paran.WU01x14 Added to gene families: 39734 33 4350 433 296.5 lotja.MG20 Added to gene families: 27433 30 5430 534 419.6 phavu.G19833 Added to gene families: 26087 64 5474 547 453.3 phach.longxuteng Added to gene families: 26846 30 5364 537 410.4 prupe.Lovell Added to gene families: 35714 19 5484 508 396.5 quisa.S10 Added to gene families: 42391 17 5305 511 324.6 sento.Myeongyun Added to gene families: 31883 42 6009 506 380.2 singl.CAF01 Added to gene families: 35790 24 5546 477 314.3 treor.RG33x02 Added to gene families: 31796 4 4953 513 357.2 vitvi.PN40024 Avg: 34543 25 5392 512 379 all_annot_sets == Proportion of initial genes retained in the "aug_extra" set: Start End Pct_kept Annotation_name 29384 28354 96.5 acacr.Acra3RX 32656 28439 87.1 aesev.CIAT22838 27650 25128 90.9 arath.Col0 37510 35696 95.2 bauva.BV-YZ2020 27288 26370 96.6 cerca.ISC453364 29074 28215 97.0 chafa.ISC494698 52872 48447 91.6 glyma.Wm82 39734 32791 82.5 lotja.MG20 50444 40713 80.7 medtr.A17_HM341 37229 24457 65.7 paran.WU01x14 26087 25814 99.0 phach.longxuteng 27433 26678 97.2 phavu.G19833 26846 24489 91.2 prupe.Lovell 35714 34162 95.7 quisa.S10 42391 29929 70.6 sento.Myeongyun 31883 29008 91.0 singl.CAF01 35790 25152 70.3 treor.RG33x02 31796 27795 87.4 vitvi.PN40024 Counts of clusters by cluster size, file 34_sup_vs_fam_consen.clust.tsv: 1 418 2 397 3 303 4 253 5 221 6 164 7 150 8 136 9 128 10 124 11 124 12 112 13 117 14 103 15 122 16 159 17 224 18 370 19 505 20 576 21 625 22 618 23 554 24 523 25 477 26 452 27 359 28 320 29 320 30 295 31 268 32 229 33 217 34 166 35 155 36 149 37 124 38 114 39 126 40 110 41 114 42 91 43 83 44 81 45 92 46 83 47 83 48 78 49 98 50 88 51 85 52 80 53 65 54 65 55 85 56 64 57 62 58 51 59 70 60 49 61 63 62 51 63 52 64 49 65 46 66 32 67 41 68 32 69 34 70 25 71 37 72 32 73 34 74 22 75 29 76 25 77 22 78 26 79 18 80 18 81 22 82 26 83 17 84 26 85 18 86 18 87 14 88 18 89 21 90 28 91 17 92 22 93 13 94 19 95 10 96 16 97 15 98 9 99 19 100 13 101 11 102 13 103 11 104 21 105 5 106 12 107 17 108 10 109 11 110 11 111 18 112 14 113 8 114 14 115 12 116 10 117 7 118 12 119 12 120 14 121 7 122 7 123 5 124 5 125 4 126 5 127 5 128 9 129 5 130 9 131 8 132 7 133 7 134 8 135 8 136 5 137 4 138 6 139 8 140 12 141 7 142 3 143 6 144 4 145 4 146 10 147 2 148 5 149 5 150 3 151 8 152 3 153 7 154 4 155 8 156 3 157 4 158 8 159 8 160 7 161 3 162 3 163 7 164 2 165 4 166 2 167 8 168 3 169 5 170 2 171 2 172 1 173 9 174 7 175 3 176 3 177 9 178 2 179 2 180 3 181 3 182 5 183 3 184 4 185 4 186 3 187 3 188 1 189 1 190 7 191 3 192 4 193 4 194 3 195 1 196 2 197 1 198 3 199 3 200 4 201 4 202 4 203 2 204 2 205 2 206 4 207 1 208 3 209 1 210 2 211 2 212 2 214 2 215 4 216 4 217 1 218 4 220 2 221 2 222 4 223 3 224 6 226 2 227 2 229 2 230 1 233 3 235 1 236 2 238 1 239 2 240 1 242 2 243 1 244 1 245 2 246 1 247 1 248 1 250 2 251 4 252 4 253 3 255 1 256 1 257 2 258 1 260 3 261 1 262 2 264 3 265 2 266 1 269 2 270 1 272 1 273 1 274 1 275 2 276 1 278 2 279 1 283 3 285 1 288 1 289 1 291 1 296 1 297 3 298 1 299 1 303 2 306 1 308 1 311 1 313 1 317 2 320 2 322 1 323 1 325 1 326 1 327 1 331 1 332 1 334 1 341 1 348 2 350 1 353 1 356 1 357 1 360 1 362 2 363 1 365 3 368 1 374 1 377 1 384 1 387 1 394 2 403 1 406 1 422 1 427 1 428 1 429 1 436 1 440 1 442 1 456 1 463 2 466 1 477 1 483 1 484 1 486 1 492 1 493 1 497 1 510 1 529 2 533 1 539 1 565 1 566 1 584 1 621 1 623 2 632 1 724 1 758 1 767 1 819 1 869 1 878 1 916 1 918 1 972 1 1091 1 1104 1 1169 1 1182 1 1317 1