Run of program pandagma-pan.sh, version 2023-09-05
Run started at: Thu Sep 14 21:27:57 CDT 2023
Run ended at:   Thu Sep 14 22:04:43 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  	1.6
strict_synt    	1
out_dir_base   	out
pctl_low       	40
pctl_med       	60
pctl_hi        	80
consen_prefix  	Arachis.pan2
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	reference
preferred_annot	Tifrunner.gnm2.ann2
work_dir       	/project/legume_project/steven.cannon/pandagma/Arachis/../work_Arachis_4_1

Output directory for this run:	out_Arachis_4_1

  Statistic           	value

== Initial clusters (containing only genes within synteny blocks)
  Cluster file        	06_syn_pan.clust.tsv
  num_of_clusters     	62350
  largest_cluster     	12
  modal_clst_size     	2
  num_at_mode         	28178
  seqs_clustered      	178569

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	75928
  largest_cluster     	46
  modal_clst_size     	4
  num_at_mode         	28310
  seqs_clustered      	233701

== Augmented-extra clusters (with sequences from extra annotation sets)
    The pctl40 set consists of orthogroups with at least 3 genes per OG (>= 5 * 40/100 sets).
  Cluster file        	18_syn_pan_aug_extra.clust.tsv
  num_of_clusters     	75928
  largest_cluster     	296
  modal_clst_size>=3  	5
  num_at_mode>=3      	22283
  seqs_clustered      	302545

== 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:   65844    90  16272  1569   1282.2  arahy.Tifrunner.gnm1.ann2
  Main:   67005    75  16374  1581   1186.2  arahy.Tifrunner.gnm2.ann1
  Main:   83107    78  16272  1479   1086.8  arahy.Tifrunner.gnm2.ann2
  Extra:  78574    75  19380  1485   1073.0  araduip.V14167K30076.gnm1.ann1

  Avg:    71364    66  16914  1536  1163    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl40 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl40:  75027    78  16272  1563   1202.2  23_syn_pan_pctl40_posn_cds.fna

== Proportion of initial genes retained in the "aug_extra" and "pctl40" sets:
  Start	End_all	End_core	Pct_kept_all	Pct_kept_core	Annotation_name
  78574	68844	68844	87.6	87.6	araduip.V14167K30076.gnm1.ann1
  62292	51094	50935	82.0	81.8	arahy.BaileyII.gnm1.ann1
  65844	53652	53379	81.5	81.1	arahy.Tifrunner.gnm1.ann2
  67005	57012	56880	85.1	84.9	arahy.Tifrunner.gnm2.ann1
  83107	71943	71242	86.6	85.7	arahy.Tifrunner.gnm2.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
  68844	46883	68.10	61.75	38.25	araduip.V14167K30076.gnm1.ann1
  51094	45412	88.88	59.81	40.19	arahy.BaileyII.gnm1.ann1
  53652	46924	87.46	61.80	38.20	arahy.Tifrunner.gnm1.ann2
  57012	53262	93.42	70.15	29.85	arahy.Tifrunner.gnm2.ann1
  71943	66226	92.05	87.22	12.78	arahy.Tifrunner.gnm2.ann2

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	28178
3	15392
4	18207
5	360
6	112
7	83
8	13
9	1
10	2
11	1
12	1

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	26916
3	19125
4	28310
5	926
6	330
7	182
8	71
9	29
10	13
11	7
12	5
13	2
14	1
15	4
16	1
17	1
19	2
28	1
29	1
46	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	15206
3	16484
4	14973
5	22283
6	4492
7	1153
8	492
9	282
10	170
11	67
12	64
13	35
14	30
15	24
16	20
17	24
18	13
19	10
20	9
21	8
22	8
23	9
24	6
25	1
26	3
27	3
28	4
29	1
30	4
31	4
32	4
33	2
34	2
35	1
36	4
38	3
40	1
41	2
42	3
43	1
44	1
46	1
48	1
50	1
51	1
54	1
55	2
57	1
59	2
60	1
68	1
82	1
86	1
88	1
96	1
115	2
116	1
121	1
174	1
296	1

# Number of annotations per pangene
bin	abcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRST
1.00	..
2.00	.................................................................................................
3.00	...............................................................................................................
4.00	.............................................................................
5.00	..........................................................................................