Run of program pandagma.sh, version 2023-03-29 Run started at: Fri Mar 31 08:15:06 CDT 2023 Run ended at: Fri Mar 31 09:13:15 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 Medicago.pan1 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method reference preferred_annot A17.gnm5.ann1_6 work_dir /scratch/scannon/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 47322 largest_cluster 12 modal_clst_size 2 num_at_mode 14941 seqs_clustered 196417 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 53389 largest_cluster 98 modal_clst_size 2 num_at_mode 14042 seqs_clustered 240685 == 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 53389 largest_cluster 2302 modal_clst_size>=6 22 num_at_mode>=6 7872 seqs_clustered 943111 == 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: 38125 96 15306 1551 1196.7 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 34417 23851 87.1 60.3 medsa.XinJiangDaYe_1.gnm1.ann1 40180 34930 23988 86.9 59.7 medsa.XinJiangDaYe_2.gnm1.ann1 39982 34770 24025 87.0 60.1 medsa.XinJiangDaYe_3.gnm1.ann1 39200 34153 23562 87.1 60.1 medsa.XinJiangDaYe_4.gnm1.ann1 5738 4722 3560 82.3 62.0 medsa.XinJiangDaYe_sc.gnm1.ann1 44623 35750 34287 80.1 76.8 medtr.A17.gnm5.ann1_6 50444 36572 35752 72.5 70.9 medtr.A17_HM341.gnm4.ann2 64157 46714 46394 72.8 72.3 medtr.HM004.gnm1.ann1 65155 47641 47399 73.1 72.7 medtr.HM010.gnm1.ann1 59567 44103 43309 74.0 72.7 medtr.HM022.gnm1.ann1 64116 47012 46701 73.3 72.8 medtr.HM023.gnm1.ann1 64342 47129 46877 73.2 72.9 medtr.HM034.gnm1.ann1 65471 47735 47459 72.9 72.5 medtr.HM050.gnm1.ann1 65413 47824 47422 73.1 72.5 medtr.HM056.gnm1.ann1 63887 46524 46130 72.8 72.2 medtr.HM058.gnm1.ann1 64405 47128 46857 73.2 72.8 medtr.HM060.gnm1.ann1 65293 47769 47529 73.2 72.8 medtr.HM095.gnm1.ann1 66976 48848 48442 72.9 72.3 medtr.HM125.gnm1.ann1 65416 47943 47700 73.3 72.9 medtr.HM129.gnm1.ann1 65712 48025 47797 73.1 72.7 medtr.HM185.gnm1.ann1 60074 43682 42777 72.7 71.2 medtr.HM324.gnm1.ann1 39027 30093 29204 77.1 74.8 medtr.R108.gnmHiC_1.ann1 55706 39627 37622 71.1 67.5 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 34417 28875 83.90 54.08 45.92 medsa.XinJiangDaYe_1.gnm1.ann1 34930 29038 83.13 54.39 45.61 medsa.XinJiangDaYe_2.gnm1.ann1 34770 28613 82.29 53.59 46.41 medsa.XinJiangDaYe_3.gnm1.ann1 34153 28184 82.52 52.79 47.21 medsa.XinJiangDaYe_4.gnm1.ann1 4722 2522 53.41 4.72 95.28 medsa.XinJiangDaYe_sc.gnm1.ann1 35750 33499 93.70 62.75 37.25 medtr.A17.gnm5.ann1_6 36572 33542 91.71 62.83 37.17 medtr.A17_HM341.gnm4.ann2 46714 35156 75.26 65.85 34.15 medtr.HM004.gnm1.ann1 47641 35297 74.09 66.11 33.89 medtr.HM010.gnm1.ann1 44103 33965 77.01 63.62 36.38 medtr.HM022.gnm1.ann1 47012 35272 75.03 66.07 33.93 medtr.HM023.gnm1.ann1 47129 35123 74.53 65.79 34.21 medtr.HM034.gnm1.ann1 47735 35317 73.99 66.15 33.85 medtr.HM050.gnm1.ann1 47824 35417 74.06 66.34 33.66 medtr.HM056.gnm1.ann1 46524 35440 76.18 66.38 33.62 medtr.HM058.gnm1.ann1 47128 35297 74.90 66.11 33.89 medtr.HM060.gnm1.ann1 47769 35274 73.84 66.07 33.93 medtr.HM095.gnm1.ann1 48848 35379 72.43 66.27 33.73 medtr.HM125.gnm1.ann1 47943 35284 73.60 66.09 33.91 medtr.HM129.gnm1.ann1 48025 35205 73.31 65.94 34.06 medtr.HM185.gnm1.ann1 43682 33731 77.22 63.18 36.82 medtr.HM324.gnm1.ann1 30093 27714 92.09 51.91 48.09 medtr.R108.gnmHiC_1.ann1 39627 31321 79.04 58.67 41.33 medtr.R108_HM340.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 8 2 14941 3 9441 4 4419 5 2712 6 5101 7 9593 8 844 9 194 10 49 11 17 12 3 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 7 2 14042 3 10965 4 6051 5 3410 6 5024 7 9728 8 2124 9 883 10 444 11 242 12 131 13 81 14 54 15 39 16 24 17 20 18 14 19 10 20 11 21 11 22 5 23 6 24 4 25 6 26 5 27 4 28 4 29 2 30 1 31 4 32 4 33 3 34 1 35 2 36 1 37 2 38 2 39 2 40 1 42 1 43 3 45 2 50 1 52 1 56 1 57 1 62 1 72 1 87 1 95 1 98 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 5 2 4018 3 3674 4 3590 5 1791 6 1211 7 898 8 741 9 670 10 582 11 576 12 570 13 653 14 883 15 1033 16 1611 17 2167 18 3505 19 1793 20 2141 21 4117 22 7872 23 2495 24 1241 25 755 26 520 27 407 28 305 29 314 30 289 31 244 32 196 33 197 34 185 35 166 36 125 37 116 38 125 39 97 40 67 41 74 42 89 43 68 44 60 45 45 46 39 47 41 48 37 49 39 50 33 51 22 52 36 53 32 54 33 55 20 56 20 57 18 58 28 59 19 60 19 61 20 62 21 63 11 64 15 65 14 66 14 67 15 68 13 69 14 70 12 71 15 72 19 73 11 74 9 75 4 76 8 77 9 78 5 79 11 80 10 81 7 82 8 83 6 84 11 85 9 86 3 87 7 88 5 89 8 90 5 91 4 92 5 93 6 94 3 95 4 96 5 97 4 98 6 99 6 100 6 101 2 102 1 103 3 104 7 105 3 106 2 107 4 108 4 109 1 110 2 111 2 112 3 113 1 114 1 115 2 116 5 118 2 119 2 120 1 121 1 122 1 123 4 124 1 125 2 126 3 127 2 128 1 129 2 130 1 131 1 132 4 133 1 134 4 135 2 136 4 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