Run of program pandagma pan, version 2026-06-29
Run started at: Tue Jun 30 09:16:03 AM CDT 2026
Run ended at:   Tue Jun 30 01:23:05 PM CDT 2026

Sequence type: nucleotide
Parameter  	value
clust_iden     	0.90
clust_cov      	0.50
extra_iden     	0.80
mcl_inflation  	1.6
strict_synt    	1
pctl_low       	25
pctl_med       	50
pctl_hi        	75
consen_prefix  	Pisum.pan1
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	reference
preferred_annot	ZW6.gnm1.ann1

Output directory for this run:	out_pandagma

  Statistic           	value

== Initial clusters (containing only genes within synteny blocks)
  Cluster file        	06_syn_pan.clust.tsv
  num_of_clusters     	25966
  largest_cluster     	7
  modal_clst_size     	3
  num_at_mode         	18676
  seqs_clustered      	71678

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	25966
  largest_cluster     	363
  modal_clst_size     	3
  num_at_mode         	18522
  seqs_clustered      	86990

== Augmented-extra clusters (with sequences from extra annotation sets)
    The pctl25 set consists of orthogroups with at least 2 genes per OG (>= 4 * 25/100 sets).
  Cluster file        	18_syn_pan_aug_extra.clust.tsv
  num_of_clusters     	25966
  largest_cluster     	453
  modal_clst_size>=2  	4
  num_at_mode>=2      	17467
  seqs_clustered      	115445

== Sequence stats for CDS files
  Class:  seqs     min max    N50    ave     annotation_name
  Main:   49597   102  21408  1353    935.8  pissa.Cameor.gnm2.ann1
  Main:   33530     6  16200  1509   1156.8  pissa.JI2822.gnm1.ann1
  Main:   47133    81  33306  1413   1117.0  pissa.ZW6.gnm1.ann1
  Extra:  44674    83  42268  1368    970.2  pissa.Cameor.gnm1.ann1

  Avg:    43733    68  28295  1410  1044    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl25 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl25:  23941   150  16200  1665   1375.4  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
  44674	26024	26024	58.3	58.3	pissa.Cameor.gnm1.ann1
  49597	31593	31593	63.7	63.7	pissa.Cameor.gnm2.ann1
  33530	29375	29375	87.6	87.6	pissa.JI2822.gnm1.ann1
  47133	28453	28453	60.4	60.4	pissa.ZW6.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
  26024	23002	88.39	88.59	11.41	pissa.Cameor.gnm1.ann1
  31593	25306	80.10	97.46	2.54	pissa.Cameor.gnm2.ann1
  29375	23359	79.52	89.96	10.04	pissa.JI2822.gnm1.ann1
  28453	23540	82.73	90.66	9.34	pissa.ZW6.gnm1.ann1

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	6804
3	18676
4	399
5	77
6	9
7	1

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	4535
3	18522
4	948
5	552
6	571
7	190
8	137
9	126
10	80
11	47
12	29
13	27
14	30
15	21
16	13
17	17
18	9
19	8
20	9
21	10
22	7
23	8
24	2
25	1
26	3
27	1
28	3
29	3
30	1
31	2
33	1
34	2
36	2
37	2
38	1
39	4
40	2
42	1
43	1
44	2
49	1
50	1
51	1
52	1
54	1
55	1
57	1
60	1
62	1
65	1
67	2
69	1
72	1
73	1
77	1
87	1
92	2
98	1
100	1
102	1
103	1
104	1
105	1
108	2
109	1
111	2
116	1
117	1
121	1
130	1
134	1
363	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	1364
3	3977
4	17467
5	804
6	529
7	439
8	456
9	187
10	120
11	118
12	109
13	55
14	30
15	41
16	37
17	25
18	16
19	22
20	10
21	17
22	13
23	9
24	5
25	5
26	10
27	7
28	7
29	5
30	2
31	2
32	1
33	3
34	4
35	1
36	2
37	1
38	1
39	2
40	1
41	1
42	5
43	1
44	6
45	3
47	1
48	2
50	1
51	1
52	1
55	2
57	1
58	1
59	1
62	1
65	1
66	1
67	1
72	2
73	1
77	2
84	1
92	1
98	2
99	1
100	2
102	2
108	1
109	3
111	4
117	1
118	1
120	1
123	1
127	1
149	1
154	1
248	1
453	1