Run of program pandagma_pan.sh, version 2023-03-29
Run started at: Fri Sep  1 12:10:40 CDT 2023
Run ended at:   Fri Sep  1 13:07:25 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  	Cicer.pan2
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	reference
preferred_annot	CDCFrontier.gnm3.ann1
work_dir       	/project/legume_project/steven.cannon/pandagma/Cicer/../work_Cicer

Output directory for this run:	out_Cicer_4_2

  Statistic           	value

== Initial clusters (containing only genes within synteny blocks)
  Cluster file        	06_syn_pan.clust.tsv
  num_of_clusters     	25132
  largest_cluster     	8
  modal_clst_size     	3
  num_at_mode         	10184
  seqs_clustered      	81100

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	25132
  largest_cluster     	48
  modal_clst_size     	4
  num_at_mode         	14870
  seqs_clustered      	103003

== 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     	25132
  largest_cluster     	513
  modal_clst_size>=2  	6
  num_at_mode>=2      	13382
  seqs_clustered      	150210

== Sequence stats for CDS files
  Class:  seqs     min max    N50    ave     annotation_name
  Main:   30880    45  26373  1530   1106.7  cicar.CDCFrontier.gnm3.ann1
  Main:   30257   150  14511  1497   1149.8  cicar.ICC4958.gnm2.ann1
  Main:   34703     9  16287  1452   1009.6  cicec.S2Drd065.gnm1.ann1
  Main:   36656    66  33411  1473   1022.3  cicre.Besev079.gnm1.ann1
  Extra:  28269   150  16026  1506   1166.4  cicar.CDCFrontier.gnm1.ann1
  Extra:  25105   135  14595  1566   1232.5  cicar.CDCFrontier.gnm2.ann1

  Avg:    30978    92  20200  1504  1114    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl25 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl25:  24518    66  16026  1593   1228.9  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
  28269	23932	23932	84.7	84.7	cicar.CDCFrontier.gnm1.ann1
  25105	23275	23275	92.7	92.7	cicar.CDCFrontier.gnm2.ann1
  30880	26474	26470	85.7	85.7	cicar.CDCFrontier.gnm3.ann1
  30257	21778	21740	72.0	71.9	cicar.ICC4958.gnm2.ann1
  34703	27533	27452	79.3	79.1	cicec.S2Drd065.gnm1.ann1
  36656	27218	27189	74.3	74.2	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
  23932	19740	82.48	78.55	21.45	cicar.CDCFrontier.gnm1.ann1
  23275	21131	90.79	84.08	15.92	cicar.CDCFrontier.gnm2.ann1
  26474	24012	90.70	95.54	4.46	cicar.CDCFrontier.gnm3.ann1
  21778	18975	87.13	75.50	24.50	cicar.ICC4958.gnm2.ann1
  27533	23531	85.46	93.63	6.37	cicec.S2Drd065.gnm1.ann1
  27218	24549	90.19	97.68	2.32	cicre.Besev079.gnm1.ann1

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	4890
3	10184
4	9564
5	456
6	35
7	2
8	1

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	1741
3	4256
4	14870
5	2645
6	581
7	331
8	235
9	140
10	70
11	58
12	38
13	30
14	13
15	18
16	16
17	8
18	11
19	6
20	7
21	9
22	4
23	7
24	3
25	4
26	1
27	4
28	4
29	4
30	2
31	1
32	3
33	1
35	1
36	1
37	4
38	1
39	1
43	1
46	1
48	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	1296
3	1381
4	1823
5	2918
6	13382
7	2455
8	612
9	276
10	190
11	158
12	173
13	100
14	54
15	51
16	31
17	34
18	25
19	15
20	14
21	14
22	12
23	9
24	16
25	12
26	2
27	8
28	8
29	7
30	6
31	6
32	5
33	1
34	1
35	2
36	1
37	2
38	1
39	1
40	1
41	4
43	1
45	1
46	1
47	1
48	1
50	1
51	3
52	1
53	1
54	1
67	2
70	1
80	1
100	1
152	1
163	1
164	1
173	1
223	1
239	1
312	1
513	1

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