Run of program pandagma-pan.sh, version 2023-08-28
Run started at: Fri Sep  1 11:01:47 CDT 2023
Run ended at:   Fri Sep  1 14:37:36 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  	Glycine.pan4
annot_str_regex	([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+
order_method   	alignment
preferred_annot	Wm82_ISU01.gnm2.ann1
work_dir       	/project/legume_project/steven.cannon/pandagma/Glycine/../work_Glycine_18_35

Output directory for this run:	out_Glycine_18_35

  Statistic           	value

== Initial clusters (containing only genes within synteny blocks)
  Cluster file        	06_syn_pan.clust.tsv
  num_of_clusters     	79893
  largest_cluster     	60
  modal_clst_size     	18
  num_at_mode         	21899
  seqs_clustered      	883959

== Augmented clusters (unanchored sequences added to the initial clusters)
  Cluster file        	12_syn_pan_aug.clust.tsv
  num_of_clusters     	86175
  largest_cluster     	134
  modal_clst_size     	18
  num_at_mode         	24678
  seqs_clustered      	943863

== Augmented-extra clusters (with sequences from extra annotation sets)
    The pctl25 set consists of orthogroups with at least 14 genes per OG (>= 53 * 25/100 sets).
  Cluster file        	18_syn_pan_aug_extra.clust.tsv
  num_of_clusters     	86175
  largest_cluster     	605
  modal_clst_size>=14 	53
  num_at_mode>=14     	4407
  seqs_clustered      	2804498

== Sequence stats for CDS files
  Class:  seqs     min max    N50    ave     annotation_name
  Main:   52783    87  16383  1572   1193.3  glyma.FiskebyIII.gnm1.ann1
  Main:   58102   150  15024  1491   1100.2  glyma.Hefeng25_IGA1002.gnm1.ann1
  Main:   57393   150  17403  1515   1113.3  glyma.Huaxia3_IGA1007.gnm1.ann1
  Main:   52840   150  16308  1515   1167.2  glyma.JD17.gnm1.ann1
  Main:   58392   150  15078  1485   1096.6  glyma.Jinyuan_IGA1006.gnm1.ann1
  Main:   47649    90  16383  1590   1236.9  glyma.Lee.gnm1.ann1
  Main:   51839   150  16290  1542   1174.2  glyma.Lee.gnm2.ann1
  Main:   57505   150  16338  1509   1116.2  glyma.Wenfeng7_IGA1001.gnm1.ann1
  Main:   57286   150  16338  1518   1119.9  glyma.Wm82_IGA1008.gnm1.ann1
  Main:   48387    63  16308  1602   1237.8  glyma.Wm82_ISU01.gnm2.ann1
  Main:   56044    87  16308  1569   1168.1  glyma.Wm82.gnm2.ann1
  Main:   52872    90  16308  1572   1155.5  glyma.Wm82.gnm4.ann1
  Main:   57474   150  16338  1503   1107.4  glyma.Zh13_IGA1005.gnm1.ann1
  Main:   52141    90  16308  1611   1275.6  glyma.Zh13.gnm1.ann1
  Main:   58150   150  14778  1503   1109.8  glyma.Zh35_IGA1004.gnm1.ann1
  Main:   57925   150  15993  1500   1101.1  glyso.F_IGA1003.gnm1.ann1
  Main:   46969    90  15327  1581   1238.0  glyso.PI483463.gnm1.ann1
  Main:   55539   150  15867  1578   1205.1  glyso.W05.gnm1.ann1
  Extra:  55362    90  19512  1416   1026.1  glycy.G1267.gnm1.ann1
  Extra:  55763    90  14457  1401   1021.8  glyd3.G1403.gnm1.ann1
  Extra:  111706    90  15420  1251    902.9  glydo.G1134.gnm1.ann1
  Extra:  56688    90  17001  1410   1020.5  glyfa.G1718.gnm1.ann1
  Extra:  58881    90  15327  1485   1087.7  glyma.58-161.gnm1.ann1
  Extra:  58040    90  16248  1494   1091.6  glyma.Amsoy.gnm1.ann1
  Extra:  55000    90  26136  1536   1117.1  glyma.DongNongNo_50.gnm1.ann1
  Extra:  58259    90  16281  1500   1095.7  glyma.FengDiHuang.gnm1.ann1
  Extra:  55926    90  23778  1602   1159.7  glyma.HanDouNo_5.gnm1.ann1
  Extra:  57976    90  15696  1476   1075.1  glyma.HeiHeNo_43.gnm1.ann1
  Extra:  58570   162  18807  1674   1281.3  glyma.Hwangkeum.gnm1.ann1
  Extra:  56750    90  23502  1602   1160.9  glyma.JiDouNo_17.gnm1.ann1
  Extra:  54792    90  19887  1533   1117.7  glyma.JinDouNo_23.gnm1.ann1
  Extra:  57792    90  16305  1491   1090.6  glyma.JuXuanNo_23.gnm1.ann1
  Extra:  55267    90  27738  1548   1125.9  glyma.KeShanNo_1.gnm1.ann1
  Extra:  56086    90  24426  1545   1124.5  glyma.PI_398296.gnm1.ann1
  Extra:  56011    90  17376  1593   1156.9  glyma.PI_548362.gnm1.ann1
  Extra:  54747    90  21267  1530   1113.9  glyma.QiHuangNo_34.gnm1.ann1
  Extra:  59588    90  16281  1512   1105.0  glyma.ShiShengChangYe.gnm1.ann1
  Extra:  55191    90  31023  1557   1132.5  glyma.TieFengNo_18.gnm1.ann1
  Extra:  58496    90  16170  1509   1101.7  glyma.TieJiaSiLiHuang.gnm1.ann1
  Extra:  55769    90  21525  1548   1127.8  glyma.TongShanTianEDan.gnm1.ann1
  Extra:  57777    90  16281  1491   1094.8  glyma.WanDouNo_28.gnm1.ann1
  Extra:  54175    72  58035  1572   1185.6  glyma.Wm82.gnm1.ann1
  Extra:  54405    90  21840  1518   1107.2  glyma.XuDouNo_1.gnm1.ann1
  Extra:  55619    90  23409  1578   1144.1  glyma.YuDouNo_22.gnm1.ann1
  Extra:  55573    77  17961  2376   1722.5  glyma.Zh13.gnm2.ann1
  Extra:  56573    90  23529  1578   1141.1  glyma.ZhangChunManCangJin.gnm1.ann1
  Extra:  54502    90  17163  1524   1108.3  glyma.Zhutwinning2.gnm1.ann1
  Extra:  54803    90  18180  1542   1121.1  glyma.ZiHuaNo_4.gnm1.ann1
  Extra:  55516    90  16779  1602   1161.9  glyso.PI_549046.gnm1.ann1
  Extra:  57920    90  16305  1518   1112.0  glyso.PI_562565.gnm1.ann1
  Extra:  57884    90  16251  1467   1076.1  glyso.PI_578357.gnm1.ann1
  Extra:  55488    90  15702  1374   1014.2  glyst.G1974.gnm1.ann1
  Extra:  54366    90  18831  1419   1036.9  glysy.G1300.gnm1.ann1

  Avg:    56727   102  18934  1538  1135    all_annot_sets

== Sequence stats for final pangene CDS files -- pctl25 and trimmed
  Class:   seqs     min max    N50    ave     annotation_name
  pctl25:  57464    93  16116  1548   1161.5  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
  55362	45356	42006	81.9	75.9	glycy.G1267.gnm1.ann1
  55763	45182	41892	81.0	75.1	glyd3.G1403.gnm1.ann1
  111706	85340	78466	76.4	70.2	glydo.G1134.gnm1.ann1
  56688	46204	42498	81.5	75.0	glyfa.G1718.gnm1.ann1
  58881	55758	54210	94.7	92.1	glyma.58-161.gnm1.ann1
  58040	55189	54067	95.1	93.2	glyma.Amsoy.gnm1.ann1
  55000	51944	50767	94.4	92.3	glyma.DongNongNo_50.gnm1.ann1
  58259	55442	54472	95.2	93.5	glyma.FengDiHuang.gnm1.ann1
  52783	50785	46775	96.2	88.6	glyma.FiskebyIII.gnm1.ann1
  55926	53160	52261	95.1	93.4	glyma.HanDouNo_5.gnm1.ann1
  58102	59169	47043	101.8	81.0	glyma.Hefeng25_IGA1002.gnm1.ann1
  57976	54986	53805	94.8	92.8	glyma.HeiHeNo_43.gnm1.ann1
  57393	56966	46687	99.3	81.3	glyma.Huaxia3_IGA1007.gnm1.ann1
  58570	53418	46691	91.2	79.7	glyma.Hwangkeum.gnm1.ann1
  52840	49712	45586	94.1	86.3	glyma.JD17.gnm1.ann1
  56750	53980	53106	95.1	93.6	glyma.JiDouNo_17.gnm1.ann1
  54792	51718	50730	94.4	92.6	glyma.JinDouNo_23.gnm1.ann1
  58392	56912	45538	97.5	78.0	glyma.Jinyuan_IGA1006.gnm1.ann1
  57792	54877	53823	95.0	93.1	glyma.JuXuanNo_23.gnm1.ann1
  55267	52271	51325	94.6	92.9	glyma.KeShanNo_1.gnm1.ann1
  47649	47428	44104	99.5	92.6	glyma.Lee.gnm1.ann1
  51839	48083	44037	92.8	84.9	glyma.Lee.gnm2.ann1
  56086	53004	51899	94.5	92.5	glyma.PI_398296.gnm1.ann1
  56011	53250	52519	95.1	93.8	glyma.PI_548362.gnm1.ann1
  54747	51680	50626	94.4	92.5	glyma.QiHuangNo_34.gnm1.ann1
  59588	56788	55752	95.3	93.6	glyma.ShiShengChangYe.gnm1.ann1
  55191	52228	51282	94.6	92.9	glyma.TieFengNo_18.gnm1.ann1
  58496	55738	54740	95.3	93.6	glyma.TieJiaSiLiHuang.gnm1.ann1
  55769	52741	51702	94.6	92.7	glyma.TongShanTianEDan.gnm1.ann1
  57777	54917	53726	95.0	93.0	glyma.WanDouNo_28.gnm1.ann1
  57505	56260	46422	97.8	80.7	glyma.Wenfeng7_IGA1001.gnm1.ann1
  54175	52803	48258	97.5	89.1	glyma.Wm82.gnm1.ann1
  56044	54435	47730	97.1	85.2	glyma.Wm82.gnm2.ann1
  52872	50930	45863	96.3	86.7	glyma.Wm82.gnm4.ann1
  57286	55900	47070	97.6	82.2	glyma.Wm82_IGA1008.gnm1.ann1
  48387	47438	44305	98.0	91.6	glyma.Wm82_ISU01.gnm2.ann1
  54405	51295	50074	94.3	92.0	glyma.XuDouNo_1.gnm1.ann1
  55619	52691	51769	94.7	93.1	glyma.YuDouNo_22.gnm1.ann1
  52141	48083	44622	92.2	85.6	glyma.Zh13.gnm1.ann1
  55573	49217	47138	88.6	84.8	glyma.Zh13.gnm2.ann1
  57474	56335	46013	98.0	80.1	glyma.Zh13_IGA1005.gnm1.ann1
  58150	55999	46165	96.3	79.4	glyma.Zh35_IGA1004.gnm1.ann1
  56573	53427	52200	94.4	92.3	glyma.ZhangChunManCangJin.gnm1.ann1
  54502	51346	50156	94.2	92.0	glyma.Zhutwinning2.gnm1.ann1
  54803	51703	50530	94.3	92.2	glyma.ZiHuaNo_4.gnm1.ann1
  57925	52405	45130	90.5	77.9	glyso.F_IGA1003.gnm1.ann1
  46969	45940	42699	97.8	90.9	glyso.PI483463.gnm1.ann1
  55516	52780	51457	95.1	92.7	glyso.PI_549046.gnm1.ann1
  57920	55265	53759	95.4	92.8	glyso.PI_562565.gnm1.ann1
  57884	54467	52572	94.1	90.8	glyso.PI_578357.gnm1.ann1
  55539	51083	46184	92.0	83.2	glyso.W05.gnm1.ann1
  55488	45870	42542	82.7	76.7	glyst.G1974.gnm1.ann1
  54366	44600	41488	82.0	76.3	glysy.G1300.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
  45356	37509	82.70	43.53	56.47	glycy.G1267.gnm1.ann1
  45182	36337	80.42	42.17	57.83	glyd3.G1403.gnm1.ann1
  85340	44257	51.86	51.36	48.64	glydo.G1134.gnm1.ann1
  46204	37226	80.57	43.20	56.80	glyfa.G1718.gnm1.ann1
  55758	51796	92.89	60.11	39.89	glyma.58-161.gnm1.ann1
  55189	51643	93.57	59.93	40.07	glyma.Amsoy.gnm1.ann1
  51944	48083	92.57	55.80	44.20	glyma.DongNongNo_50.gnm1.ann1
  55442	51917	93.64	60.25	39.75	glyma.FengDiHuang.gnm1.ann1
  50785	47616	93.76	55.26	44.74	glyma.FiskebyIII.gnm1.ann1
  53160	49840	93.75	57.84	42.16	glyma.HanDouNo_5.gnm1.ann1
  59169	55442	93.70	64.34	35.66	glyma.Hefeng25_IGA1002.gnm1.ann1
  54986	51125	92.98	59.33	40.67	glyma.HeiHeNo_43.gnm1.ann1
  56966	54819	96.23	63.61	36.39	glyma.Huaxia3_IGA1007.gnm1.ann1
  53418	44111	82.58	51.19	48.81	glyma.Hwangkeum.gnm1.ann1
  49712	47961	96.48	55.66	44.34	glyma.JD17.gnm1.ann1
  53980	50020	92.66	58.04	41.96	glyma.JiDouNo_17.gnm1.ann1
  51718	48155	93.11	55.88	44.12	glyma.JinDouNo_23.gnm1.ann1
  56912	55289	97.15	64.16	35.84	glyma.Jinyuan_IGA1006.gnm1.ann1
  54877	51309	93.50	59.54	40.46	glyma.JuXuanNo_23.gnm1.ann1
  52271	48549	92.88	56.34	43.66	glyma.KeShanNo_1.gnm1.ann1
  47428	46198	97.41	53.61	46.39	glyma.Lee.gnm1.ann1
  48083	46854	97.44	54.37	45.63	glyma.Lee.gnm2.ann1
  53004	48832	92.13	56.67	43.33	glyma.PI_398296.gnm1.ann1
  53250	49947	93.80	57.96	42.04	glyma.PI_548362.gnm1.ann1
  51680	48030	92.94	55.74	44.26	glyma.QiHuangNo_34.gnm1.ann1
  56788	52295	92.09	60.68	39.32	glyma.ShiShengChangYe.gnm1.ann1
  52228	48701	93.25	56.51	43.49	glyma.TieFengNo_18.gnm1.ann1
  55738	52371	93.96	60.77	39.23	glyma.TieJiaSiLiHuang.gnm1.ann1
  52741	48699	92.34	56.51	43.49	glyma.TongShanTianEDan.gnm1.ann1
  54917	51418	93.63	59.67	40.33	glyma.WanDouNo_28.gnm1.ann1
  56260	54734	97.29	63.51	36.49	glyma.Wenfeng7_IGA1001.gnm1.ann1
  52803	50897	96.39	59.06	40.94	glyma.Wm82.gnm1.ann1
  54435	52799	96.99	61.27	38.73	glyma.Wm82.gnm2.ann1
  50930	50002	98.18	58.02	41.98	glyma.Wm82.gnm4.ann1
  55900	54714	97.88	63.49	36.51	glyma.Wm82_IGA1008.gnm1.ann1
  47438	46680	98.40	54.17	45.83	glyma.Wm82_ISU01.gnm2.ann1
  51295	47591	92.78	55.23	44.77	glyma.XuDouNo_1.gnm1.ann1
  52691	49176	93.33	57.07	42.93	glyma.YuDouNo_22.gnm1.ann1
  48083	46805	97.34	54.31	45.69	glyma.Zh13.gnm1.ann1
  49217	42681	86.72	49.53	50.47	glyma.Zh13.gnm2.ann1
  56335	55199	97.98	64.05	35.95	glyma.Zh13_IGA1005.gnm1.ann1
  55999	54755	97.78	63.54	36.46	glyma.Zh35_IGA1004.gnm1.ann1
  53427	49569	92.78	57.52	42.48	glyma.ZhangChunManCangJin.gnm1.ann1
  51346	47538	92.58	55.16	44.84	glyma.Zhutwinning2.gnm1.ann1
  51703	48116	93.06	55.84	44.16	glyma.ZiHuaNo_4.gnm1.ann1
  52405	50953	97.23	59.13	40.87	glyso.F_IGA1003.gnm1.ann1
  45940	44897	97.73	52.10	47.90	glyso.PI483463.gnm1.ann1
  52780	49448	93.69	57.38	42.62	glyso.PI_549046.gnm1.ann1
  55265	51747	93.63	60.05	39.95	glyso.PI_562565.gnm1.ann1
  54467	50356	92.45	58.43	41.57	glyso.PI_578357.gnm1.ann1
  51083	49636	97.17	57.60	42.40	glyso.W05.gnm1.ann1
  45870	37684	82.15	43.73	56.27	glyst.G1974.gnm1.ann1
  44600	36250	81.28	42.07	57.93	glysy.G1300.gnm1.ann1

Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv:
2	10855
3	5756
4	4030
5	3129
6	2886
7	3056
8	2905
9	2423
10	2331
11	1983
12	1767
13	1792
14	1885
15	2357
16	3322
17	6901
18	21899
19	340
20	41
21	40
22	30
23	25
24	20
25	16
26	14
27	14
28	14
29	10
30	7
31	11
32	10
33	3
34	5
35	5
36	4
38	1
39	1
41	1
42	1
49	1
55	1
60	1

Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv:
2	10617
3	7349
4	4911
5	3778
6	3145
7	3200
8	3200
9	2758
10	2711
11	2176
12	1955
13	1876
14	1912
15	2304
16	3043
17	5387
18	24678
19	752
20	90
21	39
22	31
23	37
24	27
25	24
26	21
27	20
28	18
29	11
30	17
31	13
32	12
33	10
34	4
35	9
36	9
37	7
38	1
39	2
40	1
41	2
42	1
44	2
46	1
47	1
48	1
49	1
50	1
52	1
57	1
59	1
66	1
68	1
70	1
71	1
102	1
118	1
134	1

Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv:
2	3454
3	3638
4	3181
5	2880
6	2460
7	2262
8	2180
9	1865
10	1666
11	1350
12	1213
13	1005
14	883
15	823
16	741
17	626
18	641
19	600
20	569
21	568
22	563
23	496
24	559
25	554
26	529
27	569
28	656
29	701
30	706
31	750
32	794
33	791
34	854
35	798
36	829
37	869
38	896
39	831
40	881
41	858
42	905
43	917
44	1031
45	1124
46	1352
47	1629
48	1948
49	2279
50	2688
51	3202
52	3745
53	4407
54	4000
55	2483
56	1600
57	1140
58	810
59	653
60	490
61	390
62	291
63	189
64	193
65	144
66	104
67	111
68	99
69	76
70	69
71	70
72	60
73	55
74	50
75	45
76	49
77	48
78	47
79	39
80	32
81	42
82	19
83	25
84	26
85	22
86	15
87	18
88	14
89	14
90	16
91	14
92	7
93	10
94	8
95	11
96	6
97	12
98	11
99	9
100	5
101	3
102	3
103	8
104	2
105	2
106	6
107	6
108	5
109	8
110	3
111	5
112	3
113	8
114	3
115	2
116	4
117	1
118	6
119	4
120	3
121	3
122	1
123	3
124	4
125	4
126	4
127	2
128	3
129	1
131	5
132	1
133	1
134	1
135	1
136	1
137	3
138	2
139	3
140	3
141	2
144	1
145	2
147	3
148	1
149	1
150	1
151	1
152	1
153	1
154	1
155	1
156	1
157	2
158	1
159	1
160	1
162	1
163	2
167	2
169	2
170	2
171	2
172	1
175	1
179	1
181	1
184	1
185	2
190	2
191	1
198	3
201	1
207	1
210	1
212	1
217	1
223	1
224	2
227	1
232	1
235	2
238	1
248	1
250	1
252	1
253	1
256	1
258	1
274	3
278	1
283	1
297	1
309	1
326	1
327	1
336	1
355	1
384	1
410	1
424	1
430	1
437	1
441	1
468	1
491	1
494	1
500	1
605	1

# Number of annotations per pangene
bin	abcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRSTabcdefghijKLMNOPQRST
1.00	..
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28.00	.......
29.00	........
30.00	.........
31.00	.........
32.00	.........
33.00	.........
34.00	..........
35.00	.........
36.00	.........
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38.00	.........
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40.00	.........
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42.00	..........
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48.00	..........................
49.00	..................................
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