Run of program pandagma-pan.sh, version 2023-08-28
Run started at: Sat Sep  2 17:32:32 CDT 2023
Run ended at:   Sat Sep  2 17:58:16 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  	1.6
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       	/project/legume_project/steven.cannon/pandagma/Vigna/../work_Vigna_7_5

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     	29526
  largest_cluster     	14
  modal_clst_size     	7
  num_at_mode         	22969
  seqs_clustered      	187669

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	30200
  largest_cluster     	28
  modal_clst_size     	7
  num_at_mode         	23402
  seqs_clustered      	191845

== 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     	30200
  largest_cluster     	76
  modal_clst_size>=4  	12
  num_at_mode>=4      	12370
  seqs_clustered      	308214

== 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:  28687    84  23532  1617   1259.3  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	21247	21243	79.1	79.1	vigan.Gyeongwon.gnm3.ann1
  31241	23146	23146	74.1	74.1	vigan.Shumari.gnm1.ann1
  22368	19402	19401	86.7	86.7	vigra.VC1973A.gnm6.ann1
  30958	24479	24475	79.1	79.1	vigra.VC1973A.gnm7.ann1
  28297	27786	27445	98.2	97.0	vigun.CB5-2.gnm1.ann1
  29773	28095	27937	94.4	93.8	vigun.IT97K-499-35.gnm1.ann1
  31948	28669	28175	89.7	88.2	vigun.IT97K-499-35.gnm1.ann2
  28461	26998	26663	94.9	93.7	vigun.Sanzi.gnm1.ann1
  28545	27427	27074	96.1	94.8	vigun.Suvita2.gnm1.ann1
  27742	27054	26698	97.5	96.2	vigun.TZ30.gnm1.ann2
  28562	26979	26609	94.5	93.2	vigun.UCR779.gnm1.ann1
  27723	26932	26586	97.1	95.9	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
  21247	19827	93.32	65.65	34.35	vigan.Gyeongwon.gnm3.ann1
  23146	21675	93.64	71.77	28.23	vigan.Shumari.gnm1.ann1
  19402	18200	93.80	60.26	39.74	vigra.VC1973A.gnm6.ann1
  24479	21160	86.44	70.07	29.93	vigra.VC1973A.gnm7.ann1
  27786	27088	97.49	89.70	10.30	vigun.CB5-2.gnm1.ann1
  28095	26419	94.03	87.48	12.52	vigun.IT97K-499-35.gnm1.ann1
  28669	27645	96.43	91.54	8.46	vigun.IT97K-499-35.gnm1.ann2
  26998	26721	98.97	88.48	11.52	vigun.Sanzi.gnm1.ann1
  27427	27147	98.98	89.89	10.11	vigun.Suvita2.gnm1.ann1
  27054	26783	99.00	88.69	11.31	vigun.TZ30.gnm1.ann2
  26979	26777	99.25	88.67	11.33	vigun.UCR779.gnm1.ann1
  26932	26751	99.33	88.58	11.42	vigun.ZN016.gnm1.ann2

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	1725
3	1059
4	926
5	1044
6	1627
7	22969
8	95
9	35
10	24
11	11
12	8
13	1
14	2

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	1788
3	1241
4	1003
5	1030
6	1383
7	23402
8	193
9	63
10	34
11	26
12	14
13	7
14	7
15	1
16	3
17	1
22	1
24	2
28	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	1000
3	999
4	815
5	798
6	746
7	936
8	1611
9	1309
10	2317
11	4719
12	12370
13	1364
14	603
15	238
16	162
17	83
18	41
19	17
20	18
21	9
22	7
23	4
24	5
25	5
26	5
27	2
28	2
30	1
31	1
32	1
33	1
34	1
35	2
36	1
44	1
48	1
53	1
55	1
57	1
64	1
76	1

# Number of annotations per pangene
bin	abcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRST
1.00
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6.00	.....
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10.00	.................
11.00	...................................
12.00	.........................................................................................