Run of program pandagma-pan.sh, version 2023-12-17 Run started at: Wed Jan 3 07:47:53 PM CST 2024 Run ended at: Fri Jan 5 09:59:10 AM CST 2024 Sequence type: nucleotide Parameter value clust_iden 0.90 clust_cov 0.50 extra_iden 0.80 mcl_inflation 1.6 strict_synt 1 out_dir_base /project/maizegdb/ethy/pan-zea-complete/pandagma/out_Jan_24 pctl_low 25 pctl_med 50 pctl_hi 75 consen_prefix Zea.pan3 annot_str_regex (\D+\d+\D+)\d+.+ order_method reference preferred_annot Zm00001eb work_dir /project/maizegdb/ethy/pan-zea-complete/work_pan_zea_Jan_24 Output directory for this run: /project/maizegdb/ethy/pan-zea-complete/pandagma/out_Jan_24_pan_zea Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 78524 largest_cluster 146 modal_clst_size 2 num_at_mode 20731 seqs_clustered 1141084 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 87713 largest_cluster 184 modal_clst_size 2 num_at_mode 25697 seqs_clustered 1182077 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 15 genes per OG (>= 57 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 87713 largest_cluster 275 modal_clst_size>=15 56 num_at_mode>=15 5374 seqs_clustered 2026087 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 43285 48 16278 1497 1135.4 Zd-Gigi-REFERENCE-PanAnd-1. Main: 41206 48 16278 1509 1138.5 Zd-Momo-REFERENCE-PanAnd-1. Main: 36189 48 16278 1527 1170.5 Zh-RIMHU001-REFERENCE-PanAnd- Main: 39756 87 16278 1437 1088.9 Zm-B73-REFERENCE-NAM- Main: 40368 135 16278 1434 1077.9 Zm-B97-REFERENCE-NAM- Main: 40013 93 16278 1434 1080.6 Zm-CML103-REFERENCE-NAM- Main: 41577 45 16278 1422 1076.0 Zm-CML228-REFERENCE-NAM- Main: 40383 84 15201 1431 1082.4 Zm-CML247-REFERENCE-NAM- Main: 40325 105 16278 1431 1077.7 Zm-CML277-REFERENCE-NAM- Main: 41122 105 16278 1422 1067.0 Zm-CML322-REFERENCE-NAM- Main: 40428 72 16278 1431 1080.3 Zm-CML333-REFERENCE-NAM- Main: 40473 126 16278 1428 1087.6 Zm-CML52-REFERENCE-NAM- Main: 40272 120 16278 1422 1062.3 Zm-CML69-REFERENCE-NAM- Main: 39785 69 16278 1431 1085.4 Zm-HP301-REFERENCE-NAM- Main: 40290 69 16278 1425 1074.6 Zm-Il14H-REFERENCE-NAM- Main: 39868 156 16278 1437 1087.1 Zm-Ki11-REFERENCE-NAM- Main: 41059 138 16278 1422 1071.8 Zm-Ki3-REFERENCE-NAM- Main: 40778 123 16278 1425 1070.0 Zm-Ky21-REFERENCE-NAM- Main: 41486 105 16278 1416 1062.2 Zm-M162W-REFERENCE-NAM- Main: 40905 138 16278 1428 1071.6 Zm-M37W-REFERENCE-NAM- Main: 41204 75 16278 1419 1061.1 Zm-Mo18W-REFERENCE-NAM- Main: 41247 69 16278 1422 1074.6 Zm-Ms71-REFERENCE-NAM- Main: 40484 153 16278 1434 1082.6 Zm-NC350-REFERENCE-NAM- Main: 39787 117 16278 1437 1086.2 Zm-NC358-REFERENCE-NAM- Main: 39973 156 16278 1437 1082.7 Zm-Oh43-REFERENCE-NAM- Main: 40334 105 16278 1431 1078.0 Zm-Oh7B-REFERENCE-NAM- Main: 41478 99 16278 1416 1059.2 Zm-P39-REFERENCE-NAM- Main: 41164 132 16278 1419 1065.5 Zm-Tx303-REFERENCE-NAM- Main: 41593 27 16278 1419 1066.0 Zm-Tzi8-REFERENCE-NAM- Main: 29237 48 16278 1515 1147.6 Zn-PI615697-REFERENCE-PanAnd- Main: 37878 48 16278 1524 1162.3 Zv-TIL01-REFERENCE-PanAnd- Main: 40039 42 16281 1515 1147.1 Zv-TIL11-REFERENCE-PanAnd- Main: 35698 48 16278 1530 1182.0 Zx-TIL18-REFERENCE-PanAnd- Main: 36447 48 16458 1527 1167.7 Zx-TIL25-REFERENCE-PanAnd- Extra: 40747 93 16392 1485 1089.7 Zm-A188-REFERENCE-KSU- Extra: 45287 150 16269 1485 1122.0 Zm-A632-REFERENCE-CAAS_FIL- Extra: 39323 9 15804 1536 1177.7 Zm-B73-REFERENCE-GRAMENE- Extra: 42500 150 15201 1494 1140.9 Zm-Chang-7_ Extra: 43718 150 16278 1485 1124.0 Zm-Dan340-REFERENCE-CAAS_FIL- Extra: 48140 30 16278 1389 998.2 Zm-DK105-REFERENCE-TUM- Extra: 46105 30 16278 1404 1025.2 Zm-EP1-REFERENCE-TUM- Extra: 48370 30 16278 1383 999.6 Zm-F7-REFERENCE-TUM- Extra: 44771 6 16278 1488 1125.8 Zm-Huangzaosi-REFERENCE-CAAS_FIL-1. Extra: 38368 48 19343 2178 1635.7 Zm-Ia453-REFERENCE-FL- Extra: 46311 62 16278 1473 1111.9 Zm-Jing724-REFERENCE-CAAS_FIL- Extra: 45537 150 16278 1479 1120.2 Zm-Jing92-REFERENCE-CAAS_FIL- Extra: 38238 156 15465 1476 1126.0 Zm-K0326Y-REFERENCE-SIPPE- Extra: 42580 75 15201 1473 1094.2 Zm-Mo17-REFERENCE-CAU- Extra: 48306 30 16278 1389 998.0 Zm-PE0075-REFERENCE-TUM- Extra: 40557 9 14844 1404 1061.4 Zm-PH207-REFERENCE_NS-UIUC_UMN- Extra: 44719 150 16302 1479 1124.6 Zm-S37-REFERENCE-CAAS_FIL- Extra: 43271 120 16278 1530 1179.3 Zm-SK-REFERENCE-YAN-1. Extra: 40690 6 16281 1491 1141.3 Zm-W22-REFERENCE-NRGENE- Extra: 44191 150 16278 1482 1119.8 Zm-Xu178-REFERENCE-CAAS_FIL- Extra: 44791 150 16278 1482 1120.8 Zm-Ye478-REFERENCE-CAAS_FIL- Extra: 44845 150 16269 1482 1121.0 Zm-Zheng58-REFERENCE-CAAS_FIL- Extra: 39301 84 14668 1910 1558.5 Zm-B73-REFERENCE-GRAMENE- Avg: 41347 88 16204 1475 1114 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25.000000 and trimmed Class: seqs min max N50 ave annotation_name pctl25.000000: 35756 111 16278 1521 1198.7 23_syn_pan_pctl25_posn_cds.fna == Proportion of initial genes retained in the "aug_extra" and "pctl25.000000" sets: Start End_all End_core Pct_kept_all Pct_kept_core Annotation_name 43285 31478 26620 72.7 61.5 Zd00001aa 41206 33194 27907 80.6 67.7 Zd00003aa 36189 30536 27344 84.4 75.6 Zh00001aa 39301 31927 27551 81.2 70.1 5b+ 39323 36059 32427 91.7 82.5 Zm00001d 39756 35466 30266 89.2 76.1 Zm00001eb 40690 37566 31983 92.3 78.6 Zm00004b 40557 34135 29220 84.2 72.0 Zm00008a 46105 37130 32407 80.5 70.3 Zm00010a 48370 37327 32617 77.2 67.4 Zm00011a 42580 36444 31123 85.6 73.1 Zm00014ba 43271 37325 31312 86.3 72.4 Zm00015a 48140 38572 32693 80.1 67.9 Zm00016a 48306 38860 33004 80.4 68.3 Zm00017a 40368 36490 30395 90.4 75.3 Zm00018ab 40473 34613 29732 85.5 73.5 Zm00019ab 40272 35497 29942 88.1 74.3 Zm00020ab 40013 35832 30282 89.6 75.7 Zm00021ab 41577 35805 30244 86.1 72.7 Zm00022ab 40383 36057 30345 89.3 75.1 Zm00023ab 40325 35803 30259 88.8 75.0 Zm00024ab 41122 36090 30445 87.8 74.0 Zm00025ab 40428 35863 30315 88.7 75.0 Zm00026ab 39785 35689 30227 89.7 76.0 Zm00027ab 40290 35852 30177 89.0 74.9 Zm00028ab 41059 36215 30462 88.2 74.2 Zm00029ab 39868 35890 30404 90.0 76.3 Zm00030ab 40778 36626 30638 89.8 75.1 Zm00031ab 40905 36410 30544 89.0 74.7 Zm00032ab 41486 36384 30494 87.7 73.5 Zm00033ab 41204 36327 30455 88.2 73.9 Zm00034ab 41247 36327 30429 88.1 73.8 Zm00035ab 40484 36145 30490 89.3 75.3 Zm00036ab 39787 36091 30458 90.7 76.6 Zm00037ab 40334 36237 30404 89.8 75.4 Zm00038ab 39973 36065 30453 90.2 76.2 Zm00039ab 41478 36206 30226 87.3 72.9 Zm00040ab 41164 36471 30497 88.6 74.1 Zm00041ab 41593 36232 30418 87.1 73.1 Zm00042ab 38368 30453 25100 79.4 65.4 Zm00045a 38238 32781 27296 85.7 71.4 Zm00054a 40747 35852 31130 88.0 76.4 Zm00056aa 45287 38769 33809 85.6 74.7 Zm00092aa 42500 36558 32332 86.0 76.1 Zm00093aa 43718 36809 32215 84.2 73.7 Zm00094aa 44771 38139 33408 85.2 74.6 Zm00095aa 46311 38950 33750 84.1 72.9 Zm00096aa 45537 38996 34067 85.6 74.8 Zm00097aa 44719 37764 32877 84.4 73.5 Zm00100aa 44191 37429 32573 84.7 73.7 Zm00101aa 44791 37973 33154 84.8 74.0 Zm00102aa 44845 38192 33507 85.2 74.7 Zm00103aa 29237 23003 20508 78.7 70.1 Zn00001aa 37878 32129 28252 84.8 74.6 Zv00001aa 40039 32614 28365 81.5 70.8 Zv00002aa 35698 31119 27811 87.2 77.9 Zx00002aa 36447 31321 27810 85.9 76.3 Zx00003aa == 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 31478 30295 96.24 34.54 65.46 Zd00001aa 33194 31010 93.42 35.35 64.65 Zd00003aa 30536 29399 96.28 33.52 66.48 Zh00001aa 31927 28858 90.39 32.90 67.10 5b+ 36059 33685 93.42 38.40 61.60 Zm00001d 35466 34371 96.91 39.19 60.81 Zm00001eb 37566 33983 90.46 38.74 61.26 Zm00004b 34135 31655 92.73 36.09 63.91 Zm00008a 37130 34457 92.80 39.28 60.72 Zm00010a 37327 34545 92.55 39.38 60.62 Zm00011a 36444 33870 92.94 38.61 61.39 Zm00014ba 37325 34162 91.53 38.95 61.05 Zm00015a 38572 34801 90.22 39.68 60.32 Zm00016a 38860 35103 90.33 40.02 59.98 Zm00017a 36490 35514 97.33 40.49 59.51 Zm00018ab 34613 33601 97.08 38.31 61.69 Zm00019ab 35497 34507 97.21 39.34 60.66 Zm00020ab 35832 34854 97.27 39.74 60.26 Zm00021ab 35805 34788 97.16 39.66 60.34 Zm00022ab 36057 35075 97.28 39.99 60.01 Zm00023ab 35803 34834 97.29 39.71 60.29 Zm00024ab 36090 35054 97.13 39.96 60.04 Zm00025ab 35863 34873 97.24 39.76 60.24 Zm00026ab 35689 34774 97.44 39.65 60.35 Zm00027ab 35852 34832 97.15 39.71 60.29 Zm00028ab 36215 35242 97.31 40.18 59.82 Zm00029ab 35890 34895 97.23 39.78 60.22 Zm00030ab 36626 35624 97.26 40.61 59.39 Zm00031ab 36410 35372 97.15 40.33 59.67 Zm00032ab 36384 35306 97.04 40.25 59.75 Zm00033ab 36327 35331 97.26 40.28 59.72 Zm00034ab 36327 35285 97.13 40.23 59.77 Zm00035ab 36145 35097 97.10 40.01 59.99 Zm00036ab 36091 35108 97.28 40.03 59.97 Zm00037ab 36237 35302 97.42 40.25 59.75 Zm00038ab 36065 35098 97.32 40.01 59.99 Zm00039ab 36206 35120 97.00 40.04 59.96 Zm00040ab 36471 35432 97.15 40.40 59.60 Zm00041ab 36232 35207 97.17 40.14 59.86 Zm00042ab 30453 27441 90.11 31.28 68.72 Zm00045a 32781 30072 91.74 34.28 65.72 Zm00054a 35852 32684 91.16 37.26 62.74 Zm00056aa 38769 35383 91.27 40.34 59.66 Zm00092aa 36558 33693 92.16 38.41 61.59 Zm00093aa 36809 33874 92.03 38.62 61.38 Zm00094aa 38139 34877 91.45 39.76 60.24 Zm00095aa 38950 35608 91.42 40.60 59.40 Zm00096aa 38996 35612 91.32 40.60 59.40 Zm00097aa 37764 34538 91.46 39.38 60.62 Zm00100aa 37429 34350 91.77 39.16 60.84 Zm00101aa 37973 34857 91.79 39.74 60.26 Zm00102aa 38192 35080 91.85 39.99 60.01 Zm00103aa 23003 22061 95.90 25.15 74.85 Zn00001aa 32129 31002 96.49 35.34 64.66 Zv00001aa 32614 31482 96.53 35.89 64.11 Zv00002aa 31119 30218 97.10 34.45 65.55 Zx00002aa 31321 30306 96.76 34.55 65.45 Zx00003aa Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 5 2 20731 3 9036 4 5226 5 3401 6 2505 7 2022 8 1611 9 1112 10 869 11 834 12 660 13 526 14 518 15 445 16 416 17 363 18 363 19 338 20 283 21 288 22 261 23 265 24 302 25 331 26 333 27 313 28 380 29 505 30 724 31 1145 32 2274 33 6462 34 10918 35 1191 36 334 37 164 38 128 39 88 40 72 41 63 42 44 43 63 44 37 45 27 46 45 47 27 48 36 49 29 50 29 51 21 52 23 53 26 54 9 55 12 56 16 57 19 58 11 59 15 60 15 61 13 62 9 63 15 64 19 65 16 66 13 67 10 68 10 69 7 70 4 71 5 72 6 73 6 74 1 75 6 76 5 77 2 78 4 79 1 80 3 81 3 82 2 83 6 84 4 85 4 86 4 87 2 88 4 90 2 91 1 92 2 93 5 95 3 96 1 97 1 101 1 104 1 107 1 110 2 111 1 113 1 116 1 117 2 129 1 130 1 131 1 144 1 146 2 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 5 2 25697 3 10645 4 5998 5 3874 6 2752 7 2176 8 1742 9 1212 10 942 11 892 12 715 13 570 14 548 15 465 16 448 17 396 18 382 19 363 20 300 21 310 22 282 23 283 24 307 25 340 26 349 27 330 28 403 29 526 30 742 31 1163 32 2294 33 6496 34 10966 35 1201 36 336 37 164 38 130 39 88 40 73 41 63 42 44 43 64 44 37 45 29 46 47 47 28 48 37 49 31 50 29 51 21 52 25 53 26 54 9 55 12 56 16 57 19 58 13 59 15 60 15 61 14 62 11 63 15 64 19 65 16 66 13 67 11 68 10 69 7 70 5 71 5 72 6 73 6 74 1 75 6 76 6 77 3 78 4 79 1 80 3 81 3 82 2 83 6 84 4 85 4 86 4 87 2 88 4 89 1 90 2 91 1 92 2 93 5 95 3 96 1 97 1 101 1 104 1 107 1 110 2 111 1 112 1 113 1 116 1 117 2 121 1 122 1 129 1 130 1 131 1 141 1 144 1 146 2 184 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 4 2 12381 3 8185 4 5920 5 4659 6 3763 7 3101 8 2755 9 2136 10 1863 11 1637 12 1403 13 1239 14 1099 15 982 16 877 17 798 18 723 19 636 20 630 21 549 22 512 23 449 24 415 25 425 26 359 27 339 28 293 29 290 30 283 31 254 32 254 33 210 34 208 35 206 36 173 37 215 38 193 39 193 40 205 41 184 42 199 43 195 44 233 45 247 46 256 47 283 48 315 49 370 50 543 51 680 52 981 53 1511 54 2594 55 4109 56 5374 57 4668 58 1525 59 605 60 294 61 241 62 161 63 130 64 100 65 89 66 72 67 55 68 52 69 55 70 38 71 36 72 31 73 30 74 29 75 21 76 21 77 24 78 19 79 17 80 25 81 17 82 16 83 11 84 18 85 19 86 11 87 12 88 12 89 8 90 11 91 8 92 7 93 9 94 16 95 8 96 9 97 7 98 11 99 8 100 9 101 10 102 10 103 9 104 8 105 13 106 8 107 12 108 10 109 8 110 10 111 7 112 6 113 10 114 4 115 2 116 5 117 5 118 1 119 3 120 3 121 7 122 5 123 1 124 2 125 2 126 5 127 2 128 5 129 2 130 3 131 2 132 4 133 2 134 2 135 2 137 2 138 2 139 2 140 1 141 4 142 4 143 1 144 1 146 1 147 2 149 2 150 1 151 4 152 1 154 2 155 1 156 1 157 1 158 2 159 1 160 1 162 1 163 1 164 2 166 1 167 1 173 1 174 1 176 1 177 1 179 1 182 2 183 1 184 1 185 2 188 1 189 1 195 1 197 1 198 1 199 1 218 1 236 2 238 1 246 1 260 1 267 1 275 1