Run of program pandagma pan, version 2023-01-28
Run started at: Wed Jan 31 08:25:50 PM CST 2024
Run ended at:   Wed Jan 31 08:40:04 PM CST 2024

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  	Cicer.pan2
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	reference
preferred_annot	CDCFrontier.gnm3.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     	25138
  largest_cluster     	8
  modal_clst_size     	3
  num_at_mode         	10272
  seqs_clustered      	81184

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	27452
  largest_cluster     	33
  modal_clst_size     	3
  num_at_mode         	10717
  seqs_clustered      	88022

== 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     	27452
  largest_cluster     	40
  modal_clst_size>=2  	6
  num_at_mode>=2      	8845
  seqs_clustered      	129511

== Sequence stats for CDS files
  Class:  seqs     min max    N50    ave     annotation_name
  Main:   30816    45  26373  1530   1107.3  cicar.CDCFrontier.gnm3.ann1
  Main:   30148   150  14511  1497   1151.2  cicar.ICC4958.gnm2.ann1
  Main:   34557     9  16287  1452   1011.0  cicec.S2Drd065.gnm1.ann1
  Main:   36495    66  33411  1473   1023.3  cicre.Besev079.gnm1.ann1
  Extra:  28232   150  16026  1506   1167.0  cicar.CDCFrontier.gnm1.ann1
  Extra:  25103   135  14595  1566   1232.5  cicar.CDCFrontier.gnm2.ann1

  Avg:    30891    92  20200  1504  1115    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl25 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl25:  26139    66  16248  1584   1215.1  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
  28232	18949	18949	67.1	67.1	cicar.CDCFrontier.gnm1.ann1
  25103	22540	22540	89.8	89.8	cicar.CDCFrontier.gnm2.ann1
  30816	25775	25624	83.6	83.2	cicar.CDCFrontier.gnm3.ann1
  30148	14017	13700	46.5	45.4	cicar.ICC4958.gnm2.ann1
  34557	21726	21308	62.9	61.7	cicec.S2Drd065.gnm1.ann1
  36495	26504	26160	72.6	71.7	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
  18949	18064	95.33	65.80	34.20	cicar.CDCFrontier.gnm1.ann1
  22540	21630	95.96	78.79	21.21	cicar.CDCFrontier.gnm2.ann1
  25775	24980	96.92	91.00	9.00	cicar.CDCFrontier.gnm3.ann1
  14017	13411	95.68	48.85	51.15	cicar.ICC4958.gnm2.ann1
  21726	20993	96.63	76.47	23.53	cicec.S2Drd065.gnm1.ann1
  26504	25605	96.61	93.27	6.73	cicre.Besev079.gnm1.ann1

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	4762
3	10272
4	9719
5	347
6	34
7	3
8	1

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	6178
3	10717
4	9922
5	436
6	81
7	39
8	25
9	16
10	13
11	3
12	4
13	4
14	2
15	1
16	2
17	2
18	1
21	1
22	1
23	1
26	1
29	1
33	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	3074
3	2954
4	4350
5	7345
6	8845
7	537
8	152
9	67
10	37
11	23
12	14
13	14
14	10
15	5
16	4
17	4
18	4
19	2
20	1
21	2
22	1
23	1
26	1
27	1
29	1
32	1
37	1
40	1