Run of program pandagma.sh, version 2023-03-29
Run started at: Sat Apr  1 12:43:50 CDT 2023
Run ended at:   Sat Apr  1 14:06:36 CDT 2023

Sequence type: nucleotide
Parameter  	value
clust_iden     	0.95
clust_cov      	0.50
consen_iden    	0.75
extra_iden     	0.75
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  	Arachis.pan1
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	reference
preferred_annot	Tifrunner.gnm2.ann1
work_dir       	/scratch/scannon/pandagma/Arachis/../work_Arachis

Output directory for this run:	out_Arachis_5_1

  Statistic           	value

== Initial clusters (containing only genes within synteny blocks)
  Cluster file        	06_syn_pan.clust.tsv
  num_of_clusters     	69933
  largest_cluster     	10
  modal_clst_size     	2
  num_at_mode         	25278
  seqs_clustered      	222553

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	76442
  largest_cluster     	117
  modal_clst_size     	3
  num_at_mode         	20641
  seqs_clustered      	324386

== Augmented-extra clusters (with sequences from extra annotation sets)
    The pctl25 set consists of orthogroups with at least 2 genes per OG (>= 7 * 25/100 sets).
  Cluster file        	18_syn_pan_aug_extra.clust.tsv
  num_of_clusters     	76442
  largest_cluster     	247
  modal_clst_size>=2  	6
  num_at_mode>=2      	16111
  seqs_clustered      	395260

== Sequence stats for CDS files
  Class:  seqs     min max    N50    ave     annotation_name
  Main:   62292    15  16272  1566   1186.9  arahy.BaileyII.gnm1.ann1
  Main:   67124    75  16374  1584   1188.4  arahy.Tifrunner.gnm1.ann1
  Main:   65844    90  16272  1569   1282.2  arahy.Tifrunner.gnm1.ann2
  Main:   67150    75  16374  1584   1188.2  arahy.Tifrunner.gnm2.ann1
  Main:   81717    78  16272  1482   1092.1  arahy.Tifrunner.gnm2.ann2
  Extra:  78574    75  19380  1485   1073.0  araduip.V14167K30076.gnm1.ann1

  Avg:    70450    68  16824  1545  1168    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl25 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl25:  73510    75  39810  1584   1190.0  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
  36734	33174	33174	90.3	90.3	aradu.V14167.gnm1.ann1
  62292	53536	53422	85.9	85.8	arahy.BaileyII.gnm1.ann1
  67124	66699	66679	99.4	99.3	arahy.Tifrunner.gnm1.ann1
  65844	55761	54168	84.7	82.3	arahy.Tifrunner.gnm1.ann2
  67005	66771	66719	99.7	99.6	arahy.Tifrunner.gnm2.ann1
  81717	81619	79355	99.9	97.1	arahy.Tifrunner.gnm2.ann2
  41840	37700	37700	90.1	90.1	araip.K30076.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
  33174	26783	80.73	35.04	64.96	aradu.V14167.gnm1.ann1
  53536	44364	82.87	58.04	41.96	arahy.BaileyII.gnm1.ann1
  66699	57383	86.03	75.07	24.93	arahy.Tifrunner.gnm1.ann1
  55761	44031	78.96	57.60	42.40	arahy.Tifrunner.gnm1.ann2
  66771	57769	86.52	75.57	24.43	arahy.Tifrunner.gnm2.ann1
  81619	62777	76.91	82.12	17.88	arahy.Tifrunner.gnm2.ann2
  37700	29000	76.92	37.94	62.06	araip.K30076.gnm1.ann1

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
1	1
2	25278
3	22081
4	7651
5	14595
6	171
7	104
8	50
10	2

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	16559
3	20641
4	8035
5	19929
6	3257
7	1666
8	1730
9	777
10	2634
11	266
12	195
13	147
14	112
15	127
16	57
17	52
18	46
19	33
20	32
21	13
22	10
23	14
24	17
25	9
26	11
27	5
28	9
29	5
30	5
31	5
32	5
33	2
34	2
35	1
36	1
37	2
38	3
39	3
40	5
41	2
44	2
46	2
47	1
48	2
51	1
53	1
54	1
60	1
63	1
65	1
66	1
78	1
90	1
99	1
117	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	11472
3	15216
4	11183
5	8736
6	16111
7	3851
8	2109
9	1528
10	1390
11	916
12	2190
13	381
14	228
15	187
16	141
17	145
18	108
19	76
20	57
21	45
22	53
23	49
24	36
25	16
26	24
27	12
28	16
29	18
30	17
31	9
32	10
33	5
34	9
35	6
36	8
37	9
38	1
39	3
40	8
41	4
42	2
43	5
44	1
45	6
46	5
47	5
49	4
50	1
51	4
52	1
53	2
54	2
55	1
58	1
64	1
66	2
68	2
71	1
88	1
96	1
99	1
102	1
103	1
107	1
108	1
125	1
131	1
138	1
204	1
226	1
247	1