Run of program pandagma.sh, version 2023-03-29 Run started at: Fri Mar 31 16:34:05 CDT 2023 Run ended at: Fri Mar 31 17:04:20 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 Phaseolus.pan1 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method alignment preferred_annot G19833.gnm2.ann1 work_dir /scratch/scannon/pandagma/Phaseolus/../work_Phaseolus Output directory for this run: out_Phaseolus_7_1 Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 27468 largest_cluster 17 modal_clst_size 7 num_at_mode 16914 seqs_clustered 164464 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 29068 largest_cluster 236 modal_clst_size 7 num_at_mode 18251 seqs_clustered 183874 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 3 genes per OG (>= 8 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 29068 largest_cluster 241 modal_clst_size>=3 8 num_at_mode>=3 18053 seqs_clustered 210123 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 27538 171 15285 1584 1251.6 phaac.Frijol_Bayo.gnm1.ann1 Main: 27095 6 15285 1608 1231.1 phaac.W6_15578.gnm2.ann1 Main: 33734 90 16293 1620 1250.1 phalu.G27455.gnm1.ann1 Main: 27065 72 16701 1626 1302.9 phavu.5-593.gnm1.ann1 Main: 27433 90 16290 1602 1258.8 phavu.G19833.gnm2.ann1 Main: 27218 90 16359 1623 1295.4 phavu.LaborOvalle.gnm1.ann1 Main: 27385 90 16290 1626 1295.0 phavu.UI111.gnm1.ann1 Extra: 27197 96 16290 1614 1273.7 phavu.G19833.gnm1.ann1 Avg: 28083 88 16099 1612 1269 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 27497 90 16290 1662 1321.5 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 27538 25143 24901 91.3 90.4 phaac.Frijol_Bayo.gnm1.ann1 27095 24847 24482 91.7 90.4 phaac.W6_15578.gnm2.ann1 33734 28236 25473 83.7 75.5 phalu.G27455.gnm1.ann1 27065 26287 26236 97.1 96.9 phavu.5-593.gnm1.ann1 27197 26249 26249 96.5 96.5 phavu.G19833.gnm1.ann1 27433 26194 26178 95.5 95.4 phavu.G19833.gnm2.ann1 27218 26650 26557 97.9 97.6 phavu.LaborOvalle.gnm1.ann1 27385 26517 26381 96.8 96.3 phavu.UI111.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 25143 23843 94.83 82.02 17.98 phaac.Frijol_Bayo.gnm1.ann1 24847 23533 94.71 80.96 19.04 phaac.W6_15578.gnm2.ann1 28236 24007 85.02 82.59 17.41 phalu.G27455.gnm1.ann1 26287 24963 94.96 85.88 14.12 phavu.5-593.gnm1.ann1 26249 24917 94.93 85.72 14.28 phavu.G19833.gnm1.ann1 26194 25080 95.75 86.28 13.72 phavu.G19833.gnm2.ann1 26650 25063 94.05 86.22 13.78 phavu.LaborOvalle.gnm1.ann1 26517 25307 95.44 87.06 12.94 phavu.UI111.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 18 2 2703 3 1390 4 1062 5 1352 6 3576 7 16914 8 258 9 90 10 55 11 31 12 14 13 1 15 3 17 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 13 2 2381 3 1502 4 1209 5 1239 6 2513 7 18251 8 950 9 319 10 183 11 138 12 87 13 74 14 61 15 23 16 24 17 20 18 13 19 6 20 4 21 5 22 6 23 4 24 2 25 2 26 1 27 1 28 4 30 1 31 2 32 2 33 1 34 1 35 2 36 1 37 2 38 1 40 2 41 2 45 1 47 2 52 1 55 1 57 1 59 1 60 1 63 1 71 1 73 1 74 1 99 1 131 1 187 1 236 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 10 2 1863 3 1440 4 962 5 1059 6 1130 7 2511 8 18053 9 924 10 333 11 199 12 131 13 109 14 79 15 53 16 59 17 35 18 14 19 15 20 11 21 15 22 4 23 7 24 5 25 2 26 3 27 3 28 4 29 1 30 1 31 1 32 1 33 2 34 1 35 1 36 1 38 2 39 1 40 1 41 3 42 1 43 1 44 1 47 2 49 1 52 1 56 1 59 1 60 1 65 1 73 1 75 1 78 1 96 1 99 1 132 1 188 1 241 1