Run of program pandagma.sh, version 2023-03-29 Run started at: Fri Mar 31 16:35:11 CDT 2023 Run ended at: Fri Mar 31 17:10:18 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 Vigna.pan2 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method alignment preferred_annot IT97K-499-35.gnm1.ann2 work_dir /scratch/scannon/pandagma/Vigna/../work_Vigna Output directory for this run: out_Vigna_7_5 Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 29701 largest_cluster 11 modal_clst_size 7 num_at_mode 22946 seqs_clustered 187669 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 30496 largest_cluster 70 modal_clst_size 7 num_at_mode 23558 seqs_clustered 197107 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 4 genes per OG (>= 12 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 30496 largest_cluster 120 modal_clst_size>=4 12 num_at_mode>=4 12423 seqs_clustered 314451 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 28297 90 16188 1599 1240.0 vigun.CB5-2.gnm1.ann1 Main: 31948 90 16278 1602 1214.9 vigun.IT97K-499-35.gnm1.ann2 Main: 28461 90 16278 1602 1238.1 vigun.Sanzi.gnm1.ann1 Main: 28545 90 16272 1605 1239.5 vigun.Suvita2.gnm1.ann1 Main: 27742 90 16272 1602 1254.2 vigun.TZ30.gnm1.ann2 Main: 28562 90 16272 1602 1239.6 vigun.UCR779.gnm1.ann1 Main: 27723 90 16272 1605 1254.2 vigun.ZN016.gnm1.ann2 Extra: 29773 90 16278 1611 1238.7 vigun.IT97K-499-35.gnm1.ann1 Extra: 26857 18 17061 1581 1168.7 vigan.Gyeongwon.gnm3.ann1 Extra: 31241 150 16263 1518 1078.5 vigan.Shumari.gnm1.ann1 Extra: 22368 12 15450 1614 1264.3 vigra.VC1973A.gnm6.ann1 Extra: 30958 6 13857 1473 1081.7 vigra.VC1973A.gnm7.ann1 Avg: 28539 75 16061 1584 1209 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 28895 90 22818 1620 1255.5 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 26857 21310 21305 79.3 79.3 vigan.Gyeongwon.gnm3.ann1 31241 23260 23258 74.5 74.4 vigan.Shumari.gnm1.ann1 22368 19443 19443 86.9 86.9 vigra.VC1973A.gnm6.ann1 30958 24883 24863 80.4 80.3 vigra.VC1973A.gnm7.ann1 28297 27879 27593 98.5 97.5 vigun.CB5-2.gnm1.ann1 29773 28448 28365 95.5 95.3 vigun.IT97K-499-35.gnm1.ann1 31948 30514 29931 95.5 93.7 vigun.IT97K-499-35.gnm1.ann2 28461 27975 27668 98.3 97.2 vigun.Sanzi.gnm1.ann1 28545 28048 27719 98.3 97.1 vigun.Suvita2.gnm1.ann1 27742 27442 27161 98.9 97.9 vigun.TZ30.gnm1.ann2 28562 27861 27529 97.5 96.4 vigun.UCR779.gnm1.ann1 27723 27388 27103 98.8 97.8 vigun.ZN016.gnm1.ann2 == 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 21310 19879 93.28 65.19 34.81 vigan.Gyeongwon.gnm3.ann1 23260 21722 93.39 71.23 28.77 vigan.Shumari.gnm1.ann1 19443 18232 93.77 59.78 40.22 vigra.VC1973A.gnm6.ann1 24883 21228 85.31 69.61 30.39 vigra.VC1973A.gnm7.ann1 27879 27532 98.76 90.28 9.72 vigun.CB5-2.gnm1.ann1 28448 26498 93.15 86.89 13.11 vigun.IT97K-499-35.gnm1.ann1 30514 28102 92.10 92.15 7.85 vigun.IT97K-499-35.gnm1.ann2 27975 27593 98.63 90.48 9.52 vigun.Sanzi.gnm1.ann1 28048 27694 98.74 90.81 9.19 vigun.Suvita2.gnm1.ann1 27442 27143 98.91 89.01 10.99 vigun.TZ30.gnm1.ann2 27861 27428 98.45 89.94 10.06 vigun.UCR779.gnm1.ann1 27388 27094 98.93 88.84 11.16 vigun.ZN016.gnm1.ann2 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 1 2 1866 3 1122 4 941 5 1068 6 1635 7 22946 8 82 9 25 10 12 11 3 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 1 2 1712 3 1141 4 977 5 1039 6 1272 7 23558 8 341 9 128 10 73 11 44 12 41 13 20 14 55 15 13 16 13 17 11 18 8 19 7 20 6 21 6 22 3 23 1 24 6 25 2 26 3 27 1 28 2 29 3 30 3 33 1 34 1 39 1 43 1 49 1 70 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 1 2 1018 3 964 4 795 5 818 6 748 7 919 8 1645 9 1301 10 2328 11 4696 12 12423 13 1376 14 655 15 253 16 182 17 88 18 56 19 43 20 35 21 28 22 16 23 13 24 11 25 10 26 8 27 3 28 6 29 6 30 4 31 4 32 3 33 4 34 5 35 1 37 3 38 2 39 3 41 2 42 1 43 2 45 2 46 2 49 2 53 2 56 1 67 1 68 2 70 1 80 1 82 1 92 1 120 1