Run of program pandagma-pan.sh, version 2023-08-28
Run started at: Sat Sep  2 17:23:50 CDT 2023
Run ended at:   Sat Sep  2 17:47:12 CDT 2023

Sequence type: nucleotide
Parameter  	value
clust_iden     	0.90
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  	Phaseolus.pan2
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	alignment
preferred_annot	G19833.gnm2.ann1
work_dir       	/project/legume_project/steven.cannon/pandagma/Phaseolus/../work_Phaseolus

Output directory for this run:	out_Phaseolus_7_1

  Statistic           	value

== Initial clusters (containing only genes within synteny blocks)
  Cluster file        	06_syn_pan.clust.tsv
  num_of_clusters     	26790
  largest_cluster     	22
  modal_clst_size     	7
  num_at_mode         	16936
  seqs_clustered      	164464

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	28690
  largest_cluster     	78
  modal_clst_size     	7
  num_at_mode         	17819
  seqs_clustered      	177265

== Augmented-extra clusters (with sequences from extra annotation sets)
    The pctl25 set consists of orthogroups with at least 3 genes per OG (>= 8 * 25/100 sets).
  Cluster file        	18_syn_pan_aug_extra.clust.tsv
  num_of_clusters     	28690
  largest_cluster     	87
  modal_clst_size>=3  	8
  num_at_mode>=3      	17621
  seqs_clustered      	203268

== Sequence stats for CDS files
  Class:  seqs     min max    N50    ave     annotation_name
  Main:   27538   171  15285  1584   1251.6  phaac.Frijol_Bayo.gnm1.ann1
  Main:   27095     6  15285  1608   1231.1  phaac.W6_15578.gnm2.ann1
  Main:   33734    90  16293  1620   1250.1  phalu.G27455.gnm1.ann1
  Main:   27065    72  16701  1626   1302.9  phavu.5-593.gnm1.ann1
  Main:   27433    90  16290  1602   1258.8  phavu.G19833.gnm2.ann1
  Main:   27218    90  16359  1623   1295.4  phavu.LaborOvalle.gnm1.ann1
  Main:   27385    90  16290  1626   1295.0  phavu.UI111.gnm1.ann1
  Extra:  27197    96  16290  1614   1273.7  phavu.G19833.gnm1.ann1

  Avg:    28083    88  16099  1612  1269    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl25 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl25:  27580    90  18573  1665   1325.3  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
  27538	24925	24744	90.5	89.9	phaac.Frijol_Bayo.gnm1.ann1
  27095	23984	23836	88.5	88.0	phaac.W6_15578.gnm2.ann1
  33734	23452	22761	69.5	67.5	phalu.G27455.gnm1.ann1
  27065	26588	26554	98.2	98.1	phavu.5-593.gnm1.ann1
  27197	26003	26003	95.6	95.6	phavu.G19833.gnm1.ann1
  27433	25555	25548	93.2	93.1	phavu.G19833.gnm2.ann1
  27218	26467	26344	97.2	96.8	phavu.LaborOvalle.gnm1.ann1
  27385	26294	26234	96.0	95.8	phavu.UI111.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
  24925	23329	93.60	81.31	18.69	phaac.Frijol_Bayo.gnm1.ann1
  23984	22644	94.41	78.93	21.07	phaac.W6_15578.gnm2.ann1
  23452	22297	95.08	77.72	22.28	phalu.G27455.gnm1.ann1
  26588	24681	92.83	86.03	13.97	phavu.5-593.gnm1.ann1
  26003	24797	95.36	86.43	13.57	phavu.G19833.gnm1.ann1
  25555	24245	94.87	84.51	15.49	phavu.G19833.gnm2.ann1
  26467	24855	93.91	86.63	13.37	phavu.LaborOvalle.gnm1.ann1
  26294	24993	95.05	87.11	12.89	phavu.UI111.gnm1.ann1

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	2217
3	1147
4	960
5	1298
6	3571
7	16936
8	279
9	119
10	99
11	79
12	42
13	21
14	8
15	5
16	4
17	3
18	1
22	1

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	2390
3	1631
4	1277
5	1243
6	2919
7	17819
8	681
9	208
10	119
11	123
12	94
13	70
14	37
15	20
16	12
17	12
18	4
19	6
20	3
21	5
22	4
24	2
25	2
28	2
32	1
36	1
37	2
44	1
50	1
78	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	1783
3	1527
4	1087
5	1031
6	1204
7	2903
8	17621
9	729
10	226
11	136
12	100
13	88
14	84
15	62
16	28
17	17
18	10
19	11
20	10
21	5
22	3
23	3
24	4
25	1
26	2
27	2
28	1
29	1
30	1
33	3
37	1
42	1
43	1
45	1
50	1
55	1
87	1

# Number of annotations per pangene
bin	abcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRST
1.00	..
2.00	..........
3.00	........
4.00	....
5.00	.....
6.00	......
7.00	..................
8.00	......................................................................................