Run of program pandagma.sh, version 2023-03-29 Run started at: Fri Mar 31 12:03:42 CDT 2023 Run ended at: Fri Mar 31 12:23:15 CDT 2023 Sequence type: nucleotide Parameter value clust_iden 0.90 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 Cicer.pan1 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method reference preferred_annot CDCFrontier.gnm3.ann1 work_dir /scratch/scannon/pandagma/Cicer/../work_Cicer Output directory for this run: out_Cicer_4_2 Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 25366 largest_cluster 6 modal_clst_size 3 num_at_mode 10236 seqs_clustered 81098 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 28104 largest_cluster 2411 modal_clst_size 4 num_at_mode 15197 seqs_clustered 118591 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 2 genes per OG (>= 6 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 28104 largest_cluster 2416 modal_clst_size>=2 6 num_at_mode>=2 13594 seqs_clustered 169022 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 30880 45 26373 1530 1106.7 cicar.CDCFrontier.gnm3.ann1 Main: 30257 150 14511 1497 1149.8 cicar.ICC4958.gnm2.ann1 Main: 34703 9 16287 1452 1009.6 cicec.S2Drd065.gnm1.ann1 Main: 36656 66 33411 1473 1022.3 cicre.Besev079.gnm1.ann1 Extra: 28269 150 16026 1506 1166.4 cicar.CDCFrontier.gnm1.ann1 Extra: 25105 135 14595 1566 1232.5 cicar.CDCFrontier.gnm2.ann1 Avg: 30978 92 20200 1504 1114 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 26264 66 16026 1581 1201.0 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 28269 26584 26584 94.0 94.0 cicar.CDCFrontier.gnm1.ann1 25105 23847 23847 95.0 95.0 cicar.CDCFrontier.gnm2.ann1 30880 29230 28929 94.7 93.7 cicar.CDCFrontier.gnm3.ann1 30257 25040 24224 82.8 80.1 cicar.ICC4958.gnm2.ann1 34703 30208 29257 87.0 84.3 cicec.S2Drd065.gnm1.ann1 36656 34113 33450 93.1 91.3 cicre.Besev079.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 26584 20593 77.46 73.27 26.73 cicar.CDCFrontier.gnm1.ann1 23847 21726 91.11 77.31 22.69 cicar.CDCFrontier.gnm2.ann1 29230 24996 85.51 88.94 11.06 cicar.CDCFrontier.gnm3.ann1 25040 20250 80.87 72.05 27.95 cicar.ICC4958.gnm2.ann1 30208 24947 82.58 88.77 11.23 cicec.S2Drd065.gnm1.ann1 34113 25822 75.70 91.88 8.12 cicre.Besev079.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 1 2 5287 3 10236 4 9409 5 419 6 14 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 1 2 3366 3 4840 4 15197 5 2776 6 639 7 373 8 277 9 163 10 93 11 72 12 46 13 48 14 23 15 28 16 23 17 11 18 14 19 16 20 7 21 11 22 6 23 8 24 5 25 6 26 1 27 5 28 5 29 3 30 5 31 3 32 4 33 1 34 1 36 2 37 5 38 3 39 2 41 1 43 2 46 1 48 1 58 1 63 1 64 1 92 1 97 1 112 1 146 1 249 1 2046 1 2411 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 1 2 2402 3 1944 4 2232 5 3217 6 13594 7 2527 8 655 9 287 10 238 11 199 12 195 13 114 14 75 15 49 16 40 17 40 18 33 19 26 20 19 21 17 22 12 23 14 24 15 25 14 26 11 27 14 28 12 29 7 30 9 31 6 32 5 33 2 34 4 35 4 36 5 37 4 38 2 39 2 40 2 41 4 42 1 43 2 44 2 45 1 46 5 47 2 48 1 49 2 50 2 51 3 52 2 59 1 61 1 63 2 65 2 78 1 81 1 85 1 87 1 90 1 92 1 93 1 96 1 97 1 108 1 111 1 112 1 118 2 126 1 130 1 131 1 138 1 150 1 249 1 576 1 2046 1 2416 1