Run of program pandagma.sh, version 2023-03-29 Run started at: Fri Mar 31 12:53:52 CDT 2023 Run ended at: Fri Mar 31 16:03:53 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 2 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 Glycine.pan3 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method alignment preferred_annot Wm82_ISU01.gnm2.ann1 work_dir /scratch/scannon/pandagma/Glycine/../work_Glycine Output directory for this run: out_Glycine_17_35 Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 80393 largest_cluster 36 modal_clst_size 17 num_at_mode 21966 seqs_clustered 834602 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 81996 largest_cluster 267 modal_clst_size 17 num_at_mode 25144 seqs_clustered 903203 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 14 genes per OG (>= 52 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 81996 largest_cluster 681 modal_clst_size>=14 52 num_at_mode>=14 4341 seqs_clustered 2769388 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 52783 87 16383 1572 1193.3 glyma.FiskebyIII.gnm1.ann1 Main: 58102 150 15024 1491 1100.2 glyma.Hefeng25_IGA1002.gnm1.ann1 Main: 57393 150 17403 1515 1113.3 glyma.Huaxia3_IGA1007.gnm1.ann1 Main: 58392 150 15078 1485 1096.6 glyma.Jinyuan_IGA1006.gnm1.ann1 Main: 47649 90 16383 1590 1236.9 glyma.Lee.gnm1.ann1 Main: 51839 150 16290 1542 1174.2 glyma.Lee.gnm2.ann1 Main: 57505 150 16338 1509 1116.2 glyma.Wenfeng7_IGA1001.gnm1.ann1 Main: 57286 150 16338 1518 1119.9 glyma.Wm82_IGA1008.gnm1.ann1 Main: 48387 63 16308 1602 1237.8 glyma.Wm82_ISU01.gnm2.ann1 Main: 56044 87 16308 1569 1168.1 glyma.Wm82.gnm2.ann1 Main: 52872 90 16308 1572 1155.5 glyma.Wm82.gnm4.ann1 Main: 57474 150 16338 1503 1107.4 glyma.Zh13_IGA1005.gnm1.ann1 Main: 52141 90 16308 1611 1275.6 glyma.Zh13.gnm1.ann1 Main: 58150 150 14778 1503 1109.8 glyma.Zh35_IGA1004.gnm1.ann1 Main: 57926 150 15993 1500 1101.1 glyso.F_IGA1003.gnm1.ann1 Main: 46969 90 15327 1581 1238.0 glyso.PI483463.gnm1.ann1 Main: 55539 150 15867 1578 1205.1 glyso.W05.gnm1.ann1 Extra: 55362 90 19512 1416 1026.1 glycy.G1267.gnm1.ann1 Extra: 55763 90 14457 1401 1021.8 glyd3.G1403.gnm1.ann1 Extra: 111706 90 15420 1251 902.9 glydo.G1134.gnm1.ann1 Extra: 56688 90 17001 1410 1020.5 glyfa.G1718.gnm1.ann1 Extra: 58881 90 15327 1485 1087.7 glyma.58-161.gnm1.ann1 Extra: 58040 90 16248 1494 1091.6 glyma.Amsoy.gnm1.ann1 Extra: 55000 90 26136 1536 1117.1 glyma.DongNongNo_50.gnm1.ann1 Extra: 58259 90 16281 1500 1095.7 glyma.FengDiHuang.gnm1.ann1 Extra: 55926 90 23778 1602 1159.7 glyma.HanDouNo_5.gnm1.ann1 Extra: 57976 90 15696 1476 1075.1 glyma.HeiHeNo_43.gnm1.ann1 Extra: 58570 162 18807 1674 1281.3 glyma.Hwangkeum.gnm1.ann1 Extra: 56750 90 23502 1602 1160.9 glyma.JiDouNo_17.gnm1.ann1 Extra: 54792 90 19887 1533 1117.7 glyma.JinDouNo_23.gnm1.ann1 Extra: 57792 90 16305 1491 1090.6 glyma.JuXuanNo_23.gnm1.ann1 Extra: 55267 90 27738 1548 1125.9 glyma.KeShanNo_1.gnm1.ann1 Extra: 56086 90 24426 1545 1124.5 glyma.PI_398296.gnm1.ann1 Extra: 56011 90 17376 1593 1156.9 glyma.PI_548362.gnm1.ann1 Extra: 54747 90 21267 1530 1113.9 glyma.QiHuangNo_34.gnm1.ann1 Extra: 59588 90 16281 1512 1105.0 glyma.ShiShengChangYe.gnm1.ann1 Extra: 55191 90 31023 1557 1132.5 glyma.TieFengNo_18.gnm1.ann1 Extra: 58496 90 16170 1509 1101.7 glyma.TieJiaSiLiHuang.gnm1.ann1 Extra: 55769 90 21525 1548 1127.8 glyma.TongShanTianEDan.gnm1.ann1 Extra: 57777 90 16281 1491 1094.8 glyma.WanDouNo_28.gnm1.ann1 Extra: 54175 72 58035 1572 1185.6 glyma.Wm82.gnm1.ann1 Extra: 54405 90 21840 1518 1107.2 glyma.XuDouNo_1.gnm1.ann1 Extra: 55619 90 23409 1578 1144.1 glyma.YuDouNo_22.gnm1.ann1 Extra: 55573 77 17961 2376 1722.5 glyma.Zh13.gnm2.ann1 Extra: 56573 90 23529 1578 1141.1 glyma.ZhangChunManCangJin.gnm1.ann1 Extra: 54502 90 17163 1524 1108.3 glyma.Zhutwinning2.gnm1.ann1 Extra: 54803 90 18180 1542 1121.1 glyma.ZiHuaNo_4.gnm1.ann1 Extra: 55516 90 16779 1602 1161.9 glyso.PI_549046.gnm1.ann1 Extra: 57920 90 16305 1518 1112.0 glyso.PI_562565.gnm1.ann1 Extra: 57884 90 16251 1467 1076.1 glyso.PI_578357.gnm1.ann1 Extra: 55488 90 15702 1374 1014.2 glyst.G1974.gnm1.ann1 Extra: 54366 90 18831 1419 1036.9 glysy.G1300.gnm1.ann1 Avg: 56802 101 18984 1538 1134 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 57630 93 16116 1551 1161.1 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 55362 45558 42607 82.3 77.0 glycy.G1267.gnm1.ann1 55763 45359 42480 81.3 76.2 glyd3.G1403.gnm1.ann1 111706 85807 79718 76.8 71.4 glydo.G1134.gnm1.ann1 56688 46428 43290 81.9 76.4 glyfa.G1718.gnm1.ann1 58881 55840 54684 94.8 92.9 glyma.58-161.gnm1.ann1 58040 55280 54463 95.2 93.8 glyma.Amsoy.gnm1.ann1 55000 52012 51139 94.6 93.0 glyma.DongNongNo_50.gnm1.ann1 58259 55522 54850 95.3 94.1 glyma.FengDiHuang.gnm1.ann1 52783 50131 46808 95.0 88.7 glyma.FiskebyIII.gnm1.ann1 55926 53256 52632 95.2 94.1 glyma.HanDouNo_5.gnm1.ann1 58102 57384 47342 98.8 81.5 glyma.Hefeng25_IGA1002.gnm1.ann1 57976 55090 54222 95.0 93.5 glyma.HeiHeNo_43.gnm1.ann1 57393 56525 47552 98.5 82.9 glyma.Huaxia3_IGA1007.gnm1.ann1 58570 54364 48232 92.8 82.3 glyma.Hwangkeum.gnm1.ann1 56750 54070 53459 95.3 94.2 glyma.JiDouNo_17.gnm1.ann1 54792 51795 51052 94.5 93.2 glyma.JinDouNo_23.gnm1.ann1 58392 57450 47121 98.4 80.7 glyma.Jinyuan_IGA1006.gnm1.ann1 57792 54956 54162 95.1 93.7 glyma.JuXuanNo_23.gnm1.ann1 55267 52387 51690 94.8 93.5 glyma.KeShanNo_1.gnm1.ann1 47649 47196 44518 99.0 93.4 glyma.Lee.gnm1.ann1 51839 49071 45620 94.7 88.0 glyma.Lee.gnm2.ann1 56086 53092 52268 94.7 93.2 glyma.PI_398296.gnm1.ann1 56011 53323 52796 95.2 94.3 glyma.PI_548362.gnm1.ann1 54747 51780 50938 94.6 93.0 glyma.QiHuangNo_34.gnm1.ann1 59588 56868 56116 95.4 94.2 glyma.ShiShengChangYe.gnm1.ann1 55191 52333 51633 94.8 93.6 glyma.TieFengNo_18.gnm1.ann1 58496 55823 55088 95.4 94.2 glyma.TieJiaSiLiHuang.gnm1.ann1 55769 52846 52066 94.8 93.4 glyma.TongShanTianEDan.gnm1.ann1 57777 55019 54083 95.2 93.6 glyma.WanDouNo_28.gnm1.ann1 57505 56727 47872 98.6 83.2 glyma.Wenfeng7_IGA1001.gnm1.ann1 54175 52875 48908 97.6 90.3 glyma.Wm82.gnm1.ann1 56044 54777 48902 97.7 87.3 glyma.Wm82.gnm2.ann1 52872 51172 46692 96.8 88.3 glyma.Wm82.gnm4.ann1 57286 56518 48423 98.7 84.5 glyma.Wm82_IGA1008.gnm1.ann1 48387 47623 45027 98.4 93.1 glyma.Wm82_ISU01.gnm2.ann1 54405 51382 50432 94.4 92.7 glyma.XuDouNo_1.gnm1.ann1 55619 52824 52105 95.0 93.7 glyma.YuDouNo_22.gnm1.ann1 52141 49699 46531 95.3 89.2 glyma.Zh13.gnm1.ann1 55573 49607 47938 89.3 86.3 glyma.Zh13.gnm2.ann1 57474 56847 47452 98.9 82.6 glyma.Zh13_IGA1005.gnm1.ann1 58150 57299 48272 98.5 83.0 glyma.Zh35_IGA1004.gnm1.ann1 56573 53653 52719 94.8 93.2 glyma.ZhangChunManCangJin.gnm1.ann1 54502 51426 50543 94.4 92.7 glyma.Zhutwinning2.gnm1.ann1 54803 51858 50948 94.6 93.0 glyma.ZiHuaNo_4.gnm1.ann1 57925 55181 48096 95.3 83.0 glyso.F_IGA1003.gnm1.ann1 46969 46246 43677 98.5 93.0 glyso.PI483463.gnm1.ann1 55516 52854 51859 95.2 93.4 glyso.PI_549046.gnm1.ann1 57920 55359 54238 95.6 93.6 glyso.PI_562565.gnm1.ann1 57884 54595 53191 94.3 91.9 glyso.PI_578357.gnm1.ann1 55538 53357 48757 96.1 87.8 glyso.W05.gnm1.ann1 55488 46145 43258 83.2 78.0 glyst.G1974.gnm1.ann1 54366 44799 42092 82.4 77.4 glysy.G1300.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 45558 37337 81.95 45.54 54.46 glycy.G1267.gnm1.ann1 45359 36106 79.60 44.03 55.97 glyd3.G1403.gnm1.ann1 85807 43950 51.22 53.60 46.40 glydo.G1134.gnm1.ann1 46428 36981 79.65 45.10 54.90 glyfa.G1718.gnm1.ann1 55840 51230 91.74 62.48 37.52 glyma.58-161.gnm1.ann1 55280 51124 92.48 62.35 37.65 glyma.Amsoy.gnm1.ann1 52012 47521 91.37 57.96 42.04 glyma.DongNongNo_50.gnm1.ann1 55522 51359 92.50 62.64 37.36 glyma.FengDiHuang.gnm1.ann1 50131 48287 96.32 58.89 41.11 glyma.FiskebyIII.gnm1.ann1 53256 49323 92.61 60.15 39.85 glyma.HanDouNo_5.gnm1.ann1 57384 55935 97.47 68.22 31.78 glyma.Hefeng25_IGA1002.gnm1.ann1 55090 50599 91.85 61.71 38.29 glyma.HeiHeNo_43.gnm1.ann1 56525 55219 97.69 67.34 32.66 glyma.Huaxia3_IGA1007.gnm1.ann1 54364 43722 80.42 53.32 46.68 glyma.Hwangkeum.gnm1.ann1 54070 49462 91.48 60.32 39.68 glyma.JiDouNo_17.gnm1.ann1 51795 47652 92.00 58.12 41.88 glyma.JinDouNo_23.gnm1.ann1 57450 56000 97.48 68.30 31.70 glyma.Jinyuan_IGA1006.gnm1.ann1 54956 50801 92.44 61.96 38.04 glyma.JuXuanNo_23.gnm1.ann1 52387 48031 91.68 58.58 41.42 glyma.KeShanNo_1.gnm1.ann1 47196 46354 98.22 56.53 43.47 glyma.Lee.gnm1.ann1 49071 48016 97.85 58.56 41.44 glyma.Lee.gnm2.ann1 53092 48252 90.88 58.85 41.15 glyma.PI_398296.gnm1.ann1 53323 49418 92.68 60.27 39.73 glyma.PI_548362.gnm1.ann1 51780 47542 91.82 57.98 42.02 glyma.QiHuangNo_34.gnm1.ann1 56868 51722 90.95 63.08 36.92 glyma.ShiShengChangYe.gnm1.ann1 52333 48202 92.11 58.79 41.21 glyma.TieFengNo_18.gnm1.ann1 55823 51805 92.80 63.18 36.82 glyma.TieJiaSiLiHuang.gnm1.ann1 52846 48193 91.20 58.77 41.23 glyma.TongShanTianEDan.gnm1.ann1 55019 50898 92.51 62.07 37.93 glyma.WanDouNo_28.gnm1.ann1 56727 55201 97.31 67.32 32.68 glyma.Wenfeng7_IGA1001.gnm1.ann1 52875 50579 95.66 61.68 38.32 glyma.Wm82.gnm1.ann1 54777 53526 97.72 65.28 34.72 glyma.Wm82.gnm2.ann1 51172 50196 98.09 61.22 38.78 glyma.Wm82.gnm4.ann1 56518 55148 97.58 67.26 32.74 glyma.Wm82_IGA1008.gnm1.ann1 47623 46793 98.26 57.07 42.93 glyma.Wm82_ISU01.gnm2.ann1 51382 47092 91.65 57.43 42.57 glyma.XuDouNo_1.gnm1.ann1 52824 48656 92.11 59.34 40.66 glyma.YuDouNo_22.gnm1.ann1 49699 47830 96.24 58.33 41.67 glyma.Zh13.gnm1.ann1 49607 42362 85.40 51.66 48.34 glyma.Zh13.gnm2.ann1 56847 55547 97.71 67.74 32.26 glyma.Zh13_IGA1005.gnm1.ann1 57299 55367 96.63 67.52 32.48 glyma.Zh35_IGA1004.gnm1.ann1 53653 49038 91.40 59.81 40.19 glyma.ZhangChunManCangJin.gnm1.ann1 51426 47025 91.44 57.35 42.65 glyma.Zhutwinning2.gnm1.ann1 51858 47638 91.86 58.10 41.90 glyma.ZiHuaNo_4.gnm1.ann1 55181 53337 96.66 65.05 34.95 glyso.F_IGA1003.gnm1.ann1 46246 45336 98.03 55.29 44.71 glyso.PI483463.gnm1.ann1 52854 48891 92.50 59.63 40.37 glyso.PI_549046.gnm1.ann1 55359 51235 92.55 62.48 37.52 glyso.PI_562565.gnm1.ann1 54595 49843 91.30 60.79 39.21 glyso.PI_578357.gnm1.ann1 53357 51176 95.91 62.41 37.59 glyso.W05.gnm1.ann1 46145 37539 81.35 45.78 54.22 glyst.G1974.gnm1.ann1 44799 36069 80.51 43.99 56.01 glysy.G1300.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 29 2 11122 3 6165 4 4261 5 3264 6 3114 7 3283 8 3251 9 2656 10 2318 11 2075 12 2025 13 1989 14 2357 15 3350 16 6731 17 21966 18 297 19 35 20 30 21 23 22 12 23 12 24 9 25 6 26 5 27 3 28 1 29 1 30 1 31 1 36 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 24 2 8737 3 6130 4 4616 5 3498 6 3101 7 3148 8 3350 9 2868 10 2479 11 2206 12 2048 13 1961 14 2193 15 2997 16 4748 17 25144 18 1646 19 251 20 97 21 59 22 38 23 43 24 39 25 31 26 34 27 27 28 28 29 27 30 29 31 19 32 39 33 45 34 202 35 23 36 8 37 3 38 5 39 3 40 4 41 4 42 1 43 2 44 2 45 1 46 1 47 1 48 3 50 4 51 4 52 2 54 3 55 2 56 1 57 1 58 1 59 3 60 1 61 3 63 1 67 1 68 1 78 2 88 1 144 1 267 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 11 2 2884 3 2873 4 2621 5 2400 6 2187 7 2072 8 2022 9 1738 10 1529 11 1288 12 1147 13 937 14 871 15 746 16 706 17 590 18 573 19 619 20 545 21 553 22 541 23 495 24 526 25 502 26 522 27 583 28 577 29 652 30 686 31 672 32 777 33 788 34 802 35 832 36 865 37 837 38 808 39 810 40 846 41 928 42 925 43 1012 44 1116 45 1304 46 1622 47 1924 48 2242 49 2709 50 3084 51 3779 52 4341 53 4113 54 2546 55 1663 56 1195 57 827 58 715 59 552 60 438 61 301 62 221 63 198 64 154 65 127 66 116 67 108 68 96 69 91 70 68 71 59 72 68 73 57 74 66 75 50 76 49 77 51 78 54 79 37 80 38 81 27 82 32 83 22 84 26 85 24 86 26 87 22 88 23 89 21 90 18 91 18 92 13 93 18 94 18 95 19 96 18 97 15 98 19 99 19 100 33 101 40 102 30 103 40 104 32 105 27 106 32 107 15 108 12 109 16 110 10 111 12 112 8 113 8 114 4 115 9 116 4 117 2 118 9 119 5 120 7 121 4 122 6 123 1 124 4 125 3 126 2 127 3 128 1 129 4 130 2 132 2 133 3 134 2 135 2 137 2 138 3 139 1 140 2 141 5 142 3 143 2 144 2 145 3 146 1 147 2 148 2 149 1 150 1 152 4 154 1 155 1 157 1 160 4 161 3 166 1 167 6 168 2 169 2 170 2 171 2 173 1 174 1 175 1 176 1 179 1 185 1 187 2 192 2 193 3 194 1 200 1 202 2 205 1 206 2 211 2 216 1 218 1 220 1 221 1 223 2 225 1 226 1 227 1 233 1 235 1 237 1 242 1 247 1 249 1 258 1 263 1 267 1 268 1 269 1 274 1 278 1 279 1 281 1 297 1 303 1 321 1 331 1 339 1 340 1 341 2 342 1 351 1 358 1 366 1 379 1 393 1 404 1 408 1 433 1 494 1 587 1 593 1 667 1 681 1