Run of program pandagma-pan.sh, version 2023-08-28 Run started at: Fri Sep 1 12:22:20 CDT 2023 Run ended at: Fri Sep 1 13:02:37 CDT 2023 Sequence type: nucleotide Parameter value clust_iden 0.95 clust_cov 0.50 consen_iden 0.80 extra_iden 0.80 mcl_inflation 1.6 strict_synt 1 dagchainer_args -g 10000 -M 50 -D 200000 -E 1e-5 -A 6 -s out_dir_base out pctl_low 25 pctl_med 50 pctl_hi 75 consen_prefix Medicago.pan1 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method reference preferred_annot A17.gnm5.ann1_6 work_dir /project/legume_project/steven.cannon/pandagma/Medicago/../work_Medicago_7_16 Output directory for this run: out_Medicago_7_16 Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 45913 largest_cluster 14 modal_clst_size 2 num_at_mode 13576 seqs_clustered 196417 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 52517 largest_cluster 105 modal_clst_size 2 num_at_mode 14541 seqs_clustered 226973 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 6 genes per OG (>= 23 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 52517 largest_cluster 2209 modal_clst_size>=6 22 num_at_mode>=6 8106 seqs_clustered 879004 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 44623 123 16089 1476 1017.7 medtr.A17.gnm5.ann1_6 Main: 50444 51 16158 1455 990.3 medtr.A17_HM341.gnm4.ann2 Main: 39027 150 15306 1482 1103.0 medtr.R108.gnmHiC_1.ann1 Main: 39532 150 18939 1521 1177.1 medsa.XinJiangDaYe_1.gnm1.ann1 Main: 40180 150 15978 1527 1177.1 medsa.XinJiangDaYe_2.gnm1.ann1 Main: 39982 150 44046 1521 1178.1 medsa.XinJiangDaYe_3.gnm1.ann1 Main: 39200 150 16056 1518 1177.0 medsa.XinJiangDaYe_4.gnm1.ann1 Extra: 5738 150 11574 1314 986.0 medsa.XinJiangDaYe_sc.gnm1.ann1 Extra: 55706 9 15882 1290 829.9 medtr.R108_HM340.gnm1.ann1 Extra: 64157 30 15306 1437 983.0 medtr.HM004.gnm1.ann1 Extra: 65155 31 15306 1446 987.6 medtr.HM010.gnm1.ann1 Extra: 59567 30 16206 1440 984.0 medtr.HM022.gnm1.ann1 Extra: 64116 30 15306 1431 974.5 medtr.HM023.gnm1.ann1 Extra: 64342 31 15306 1449 985.5 medtr.HM034.gnm1.ann1 Extra: 65471 31 15306 1443 989.4 medtr.HM050.gnm1.ann1 Extra: 65413 31 16158 1449 984.8 medtr.HM056.gnm1.ann1 Extra: 63887 30 16209 1419 970.8 medtr.HM058.gnm1.ann1 Extra: 64405 31 15306 1440 982.5 medtr.HM060.gnm1.ann1 Extra: 65293 30 15306 1440 982.5 medtr.HM095.gnm1.ann1 Extra: 66976 32 15306 1455 990.0 medtr.HM125.gnm1.ann1 Extra: 65416 31 16206 1449 989.8 medtr.HM129.gnm1.ann1 Extra: 65712 31 15306 1446 987.5 medtr.HM185.gnm1.ann1 Extra: 60074 30 16644 1398 954.3 medtr.HM324.gnm1.ann1 Avg: 54539 65 16921 1445 1016 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 37349 96 15306 1548 1200.8 23_syn_pan_pctl25_posn_cds.fna == Proportion of initial genes retained in the "aug_extra" and "pctl25" sets: Start End_all End_core Pct_kept_all Pct_kept_core Annotation_name 39532 32683 22415 82.7 56.7 medsa.XinJiangDaYe_1.gnm1.ann1 40180 32806 22397 81.6 55.7 medsa.XinJiangDaYe_2.gnm1.ann1 39982 32703 22372 81.8 56.0 medsa.XinJiangDaYe_3.gnm1.ann1 39200 31870 21773 81.3 55.5 medsa.XinJiangDaYe_4.gnm1.ann1 5738 4393 3171 76.6 55.3 medsa.XinJiangDaYe_sc.gnm1.ann1 44623 35317 33954 79.1 76.1 medtr.A17.gnm5.ann1_6 50444 33808 32929 67.0 65.3 medtr.A17_HM341.gnm4.ann2 64157 43422 43086 67.7 67.2 medtr.HM004.gnm1.ann1 65155 44092 43849 67.7 67.3 medtr.HM010.gnm1.ann1 59567 41148 40329 69.1 67.7 medtr.HM022.gnm1.ann1 64116 43681 43350 68.1 67.6 medtr.HM023.gnm1.ann1 64342 43707 43459 67.9 67.5 medtr.HM034.gnm1.ann1 65471 44129 43859 67.4 67.0 medtr.HM050.gnm1.ann1 65413 44278 43860 67.7 67.1 medtr.HM056.gnm1.ann1 63887 43312 42886 67.8 67.1 medtr.HM058.gnm1.ann1 64405 43721 43440 67.9 67.4 medtr.HM060.gnm1.ann1 65293 44200 43943 67.7 67.3 medtr.HM095.gnm1.ann1 66976 44986 44540 67.2 66.5 medtr.HM125.gnm1.ann1 65416 44334 44054 67.8 67.3 medtr.HM129.gnm1.ann1 65712 44248 44009 67.3 67.0 medtr.HM185.gnm1.ann1 60074 40725 39788 67.8 66.2 medtr.HM324.gnm1.ann1 39027 27786 27069 71.2 69.4 medtr.R108.gnmHiC_1.ann1 55706 37655 35725 67.6 64.1 medtr.R108_HM340.gnm1.ann1 == 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 32683 27566 84.34 52.49 47.51 medsa.XinJiangDaYe_1.gnm1.ann1 32806 27688 84.40 52.72 47.28 medsa.XinJiangDaYe_2.gnm1.ann1 32703 27334 83.58 52.05 47.95 medsa.XinJiangDaYe_3.gnm1.ann1 31870 26920 84.47 51.26 48.74 medsa.XinJiangDaYe_4.gnm1.ann1 4393 2436 55.45 4.64 95.36 medsa.XinJiangDaYe_sc.gnm1.ann1 35317 32691 92.56 62.25 37.75 medtr.A17.gnm5.ann1_6 33808 32134 95.05 61.19 38.81 medtr.A17_HM341.gnm4.ann2 43422 34295 78.98 65.30 34.70 medtr.HM004.gnm1.ann1 44092 34443 78.12 65.58 34.42 medtr.HM010.gnm1.ann1 41148 33204 80.69 63.23 36.77 medtr.HM022.gnm1.ann1 43681 34472 78.92 65.64 34.36 medtr.HM023.gnm1.ann1 43707 34308 78.50 65.33 34.67 medtr.HM034.gnm1.ann1 44129 34457 78.08 65.61 34.39 medtr.HM050.gnm1.ann1 44278 34610 78.17 65.90 34.10 medtr.HM056.gnm1.ann1 43312 34622 79.94 65.93 34.07 medtr.HM058.gnm1.ann1 43721 34486 78.88 65.67 34.33 medtr.HM060.gnm1.ann1 44200 34408 77.85 65.52 34.48 medtr.HM095.gnm1.ann1 44986 34573 76.85 65.83 34.17 medtr.HM125.gnm1.ann1 44334 34492 77.80 65.68 34.32 medtr.HM129.gnm1.ann1 44248 34407 77.76 65.52 34.48 medtr.HM185.gnm1.ann1 40725 33016 81.07 62.87 37.13 medtr.HM324.gnm1.ann1 27786 26380 94.94 50.23 49.77 medtr.R108.gnmHiC_1.ann1 37655 30739 81.63 58.53 41.47 medtr.R108_HM340.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 13576 3 8897 4 4307 5 2734 6 5184 7 9818 8 974 9 278 10 80 11 37 12 20 13 7 14 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 14541 3 11263 4 5701 5 3145 6 4884 7 10046 8 1832 9 617 10 239 11 112 12 57 13 27 14 16 15 6 16 7 17 5 18 5 19 3 20 2 21 1 22 1 23 1 24 1 29 1 43 1 50 1 66 1 105 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 4152 3 4003 4 3640 5 1813 6 1125 7 813 8 675 9 629 10 527 11 504 12 563 13 646 14 883 15 988 16 1554 17 2146 18 3326 19 1809 20 2163 21 4218 22 8106 23 2546 24 1182 25 671 26 470 27 335 28 267 29 257 30 232 31 188 32 199 33 159 34 150 35 131 36 107 37 109 38 85 39 62 40 65 41 68 42 61 43 54 44 41 45 35 46 29 47 35 48 34 49 20 50 18 51 30 52 19 53 24 54 11 55 17 56 13 57 12 58 16 59 20 60 11 61 6 62 17 63 11 64 9 65 7 66 11 67 8 68 10 69 7 70 11 71 6 72 10 73 5 74 10 75 9 76 5 77 1 78 3 79 8 80 11 81 6 82 5 83 5 84 10 85 4 86 2 87 6 88 3 89 1 90 3 91 3 92 4 93 3 94 2 95 1 96 2 97 3 99 2 100 1 101 4 102 5 103 1 104 2 105 3 106 2 107 2 108 2 109 4 110 2 111 3 112 2 113 3 114 4 115 2 116 2 117 3 118 3 119 2 121 1 122 2 124 1 126 3 127 1 129 1 130 3 131 1 132 1 133 2 134 2 135 4 136 5 137 1 138 3 139 2 140 1 142 3 143 2 145 1 147 3 148 2 149 2 150 1 152 3 153 1 157 2 159 1 160 1 161 1 163 1 166 3 169 2 171 1 172 2 173 3 174 1 175 1 176 1 178 1 180 2 181 1 183 1 184 3 189 1 191 1 193 2 194 1 200 1 201 2 206 1 210 1 212 1 214 2 218 2 237 1 239 1 242 1 243 1 246 1 255 2 256 1 258 1 260 2 261 2 262 2 264 2 268 1 278 1 281 1 286 1 291 1 295 1 296 1 309 1 311 1 318 1 326 1 329 1 336 1 340 2 341 1 343 1 345 1 349 1 350 1 358 2 361 1 363 1 365 1 368 1 375 2 377 1 383 1 408 1 421 1 430 1 441 1 444 1 446 1 481 1 492 1 534 1 576 1 577 1 580 1 588 1 613 1 621 1 660 1 662 1 759 1 1018 1 1145 1 1196 1 1243 1 1364 1 1606 1 1753 1 2030 1 2209 1 # Number of annotations per pangene bin abcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRST 1.00 .................. 2.00 ................................................ 3.00 ..................................... 4.00 ................................ 5.00 ............ 6.00 ........ 7.00 ....... 8.00 ...... 9.00 ...... 10.00 ..... 11.00 ...... 12.00 ....... 13.00 ........ 14.00 ........... 15.00 ................ 16.00 ........................... 17.00 ................................. 18.00 ........................................ 19.00 ................ 20.00 ............................. 21.00 ........................................................ 22.00 ..................................................................................... 23.00 .