Run of program pandagma fam, version 2023-02-23 Run started at: Mon 26 Feb 2024 11:19:43 AM PST Run ended at: Tue 27 Feb 2024 06:25:23 PM PST Parameter value clust_iden 0.40 clust_cov 0.40 extra_iden 0.30 TE_match_iden 0.40 mcl_inflation 1.6 strict_synt 1 ks_low_cutoff 0.50 ks_hi_cutoff 2.0 ks_binsize 0.05 ks_block_wgd_cutoff 1.75 max_pair_ks 4.0 consen_prefix Legume.fam3. annot_str_regex ([^.]+\.[^.]+)\..+ min_align_count 4 min_annots_in_align 2 Output directory for this run: out_pandagma == Sequence stats for protein files Class: seqs min max N50 ave annotation_name Main: 29399 4 5489 520 408.0 acacr.Acra3RX Main: 32676 49 5431 540 403.2 aesev.CIAT22838 Main: 68882 25 5458 526 408.7 Arachis.pan3 Main: 27311 26 5513 552 429.9 cerca.ISC453364 Main: 29000 31 5485 536 427.3 chafa.ISC494698 Main: 26134 22 5415 525 402.0 Cicer.pan3 Main: 30308 38 5214 492 373.7 dalod.SKLTGB Main: 57664 33 5412 510 381.4 Glycine.pan5 Main: 24735 51 5434 536 432.1 labpu.Highworth Main: 38256 3 5098 481 359.4 lencu.CDC_Redberry Main: 39584 33 4350 433 296.9 lotja.MG20 Main: 38088 40 5101 511 370.1 lupal.Amiga Main: 38493 31 5101 512 393.2 Medicago.pan3 Main: 26032 64 5474 547 453.7 phach.longxuteng Main: 25743 33 5432 546 439.8 Phaseolus.pan3 Main: 44635 27 14089 456 322.4 pissa.Cameor Main: 35789 19 5484 508 396.7 quisa.S10 Main: 44724 17 5305 505 317.0 sento.Myeongyun Main: 31892 42 6009 506 380.2 singl.CAF01 Main: 39676 1 5102 491 345.0 tripr.MilvusB Main: 34324 75 5397 485 376.5 vicfa.Hedin2 Main: 28666 27 5094 535 415.5 Vigna.pan3 Extra: 27651 4 5401 515 405.9 arath.Col0 Extra: 26855 30 5364 537 410.4 prupe.Lovell Extra: 31799 4 4953 513 357.2 vitvi.PN40024 Avg: 35132 29 5664 512 388 all_annot_sets == Proportion of initial genes retained in the "aug_extra" set: Start End Pct_kept Annotation_name 29399 28003 95.3 acacr.Acra3RX 32676 29687 90.9 aesev.CIAT22838 68882 65771 95.5 Arachis.pan3 27651 24048 87.0 arath.Col0 27311 26159 95.8 cerca.ISC453364 29000 27984 96.5 chafa.ISC494698 26134 24947 95.5 Cicer.pan3 30308 27508 90.8 dalod.SKLTGB 57664 54199 94.0 Glycine.pan5 24735 24488 99.0 labpu.Highworth 38256 36048 94.2 lencu.CDC_Redberry 39584 33558 84.8 lotja.MG20 38088 34752 91.2 lupal.Amiga 38493 35496 92.2 Medicago.pan3 26032 25581 98.3 phach.longxuteng 25743 25455 98.9 Phaseolus.pan3 44635 36745 82.3 pissa.Cameor 26855 23979 89.3 prupe.Lovell 35789 33671 94.1 quisa.S10 44724 34283 76.7 sento.Myeongyun 31892 28147 88.3 singl.CAF01 39676 35256 88.9 tripr.MilvusB 34324 31585 92.0 vicfa.Hedin2 28666 27436 95.7 Vigna.pan3 31799 26684 83.9 vitvi.PN40024 == For all annotation sets, counts of genes-in-orthogroups and counts of orthogroups-with-genes: gns-in-OGs OGs-w-gns OGs-w-gns/gns pct-non-null-OGs pct-null-OGs annot-set 65771 19206 29.20 48.04 51.96 Arachis.pan3 24947 17705 70.97 44.28 55.72 Cicer.pan3 54199 19411 35.81 48.55 51.45 Glycine.pan5 35496 19076 53.74 47.71 52.29 Medicago.pan3 25455 17357 68.19 43.41 56.59 Phaseolus.pan3 27436 17797 64.87 44.51 55.49 Vigna.pan3 28003 16977 60.63 42.46 57.54 acacr.Acra3RX 29687 17382 58.55 43.48 56.52 aesev.CIAT22838 24048 14597 60.70 36.51 63.49 arath.Col0 26159 18379 70.26 45.97 54.03 cerca.ISC453364 27984 17357 62.02 43.41 56.59 chafa.ISC494698 27508 17670 64.24 44.20 55.80 dalod.SKLTGB 24488 16904 69.03 42.28 57.72 labpu.Highworth 36048 18279 50.71 45.72 54.28 lencu.CDC_Redberry 33558 18555 55.29 46.41 53.59 lotja.MG20 34752 17384 50.02 43.48 56.52 lupal.Amiga 25581 15493 60.56 38.75 61.25 phach.longxuteng 36745 19582 53.29 48.98 51.02 pissa.Cameor 23979 16596 69.21 41.51 58.49 prupe.Lovell 33671 17799 52.86 44.52 55.48 quisa.S10 34283 17947 52.35 44.89 55.11 sento.Myeongyun 28147 17145 60.91 42.88 57.12 singl.CAF01 35256 19414 55.07 48.56 51.44 tripr.MilvusB 31585 18105 57.32 45.28 54.72 vicfa.Hedin2 26684 16311 61.13 40.80 59.20 vitvi.PN40024 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 8215 3 3758 4 2217 5 1580 6 1249 7 1016 8 802 9 707 10 609 11 489 12 461 13 345 14 341 15 308 16 301 17 334 18 310 19 311 20 299 21 300 22 296 23 316 24 334 25 423 26 554 27 657 28 780 29 808 30 846 31 746 32 667 33 649 34 552 35 485 36 453 37 483 38 377 39 369 40 314 41 305 42 271 43 328 44 269 45 273 46 252 47 256 48 268 49 242 50 242 51 248 52 216 53 233 54 215 55 200 56 149 57 155 58 124 59 115 60 98 61 105 62 96 63 76 64 55 65 72 66 48 67 54 68 42 69 39 70 34 71 48 72 27 73 29 74 35 75 30 76 21 77 25 78 22 79 21 80 16 81 23 82 11 83 14 84 7 85 13 86 15 87 10 88 16 89 15 90 9 91 9 92 9 93 10 94 4 95 16 96 10 97 10 98 13 99 9 100 4 101 9 102 10 103 9 104 6 105 4 106 4 107 10 108 10 109 7 110 8 111 2 112 9 113 6 114 5 115 5 116 2 117 3 118 1 119 4 120 1 121 3 122 5 123 5 124 6 125 3 126 2 127 3 128 3 129 3 130 4 131 4 132 6 133 2 134 5 135 1 136 2 137 2 138 1 139 3 140 6 141 4 142 5 143 3 144 2 145 1 147 3 148 2 149 2 150 5 151 2 152 1 153 1 154 2 155 1 156 3 157 4 158 1 159 2 160 4 161 1 162 3 163 3 164 1 165 6 166 1 167 1 168 3 169 2 171 2 172 2 173 1 174 3 175 1 176 1 177 1 178 1 179 1 180 1 181 2 183 1 184 2 185 1 186 1 187 1 188 1 190 1 191 2 192 1 193 1 194 3 198 1 200 1 202 1 204 1 205 1 206 2 207 3 209 1 213 1 214 2 216 2 217 1 218 1 220 1 227 3 230 1 232 1 233 1 234 2 237 1 241 1 244 1 247 1 248 1 249 1 259 1 262 1 263 1 267 1 268 1 269 1 271 1 273 1 276 1 285 1 289 2 291 1 370 1 372 1 387 1 389 2 392 1 409 1 652 1 992 1