-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_37

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_37-snap.5-T1
Couldn't classify 2101, 2232
Sorry, prediction pasa_asmbl_41009.p1 fails validation.
(AGT)	 TC	2101-2232	GT	AGG
(GTC)	 AG	2483-2593	GT	AGG
(GTG)	 AG	2804-2955	GT	AGG
(GCT)	 AG	3092-3272	GT	AGG
(GTA)	 AG	3645-3746	GT	AGG
(GTC)	 AG	3866-3964	GT	AGG
(GTG)	 AG	4203-4283	CT	AGC
-recovered pasa_asmbl_41009.p1, terminal, 4203, 4283
-recovered pasa_asmbl_41009.p1, internal, 2483, 2593
-recovered pasa_asmbl_41009.p1, internal, 2804, 2955
-recovered pasa_asmbl_41009.p1, internal, 3092, 3272
-recovered pasa_asmbl_41009.p1, internal, 3645, 3746
-recovered pasa_asmbl_41009.p1, internal, 3866, 3964
Valid prediction for Augustus_model.g40573.t1
Couldn't classify 455, 499
Sorry, prediction snap_scaffold_37-snap.2-T1 fails validation.
(AGG)	 AG	455-499	GT	TCG
(TTG)	 AG	2103-2232	GT	AGG
(GTC)	 AG	2483-2593	GT	AGG
(GTG)	 AG	2804-2955	GT	AGG
(GCT)	 AG	3092-3272	GT	AGG
(GTA)	 AG	3645-3746	GT	AGG
(GTC)	 AG	3866-3964	GT	AGG
(GCT)	 AG	3969-4055	AA	AAA
-recovered snap_scaffold_37-snap.2-T1, terminal, 3969, 4055
-recovered snap_scaffold_37-snap.2-T1, internal, 455, 499
-recovered snap_scaffold_37-snap.2-T1, internal, 2103, 2232
-recovered snap_scaffold_37-snap.2-T1, internal, 2483, 2593
-recovered snap_scaffold_37-snap.2-T1, internal, 2804, 2955
-recovered snap_scaffold_37-snap.2-T1, internal, 3092, 3272
-recovered snap_scaffold_37-snap.2-T1, internal, 3645, 3746
-recovered snap_scaffold_37-snap.2-T1, internal, 3866, 3964
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_37-snap.6-T1
Valid prediction for GeneMark_model.106190_t
Couldn't classify 455, 474
Sorry, prediction Augustus_model.g40571.t1 fails validation.
(AGG)	 AG	455-474	GT	AGG
(TTG)	 AG	2103-2232	GT	AGG
(GTC)	 AG	2483-2593	GT	AGG
(GTG)	 AG	2804-2955	GT	AGG
(GCT)	 AG	3092-3272	GT	AGG
(GTA)	 AG	3645-3746	GT	AGG
(GTC)	 AG	3866-3964	GT	AGG
(GTG)	 AG	4203-4283	CT	AGC
-recovered Augustus_model.g40571.t1, terminal, 4203, 4283
-recovered Augustus_model.g40571.t1, internal, 455, 474
-recovered Augustus_model.g40571.t1, internal, 2103, 2232
-recovered Augustus_model.g40571.t1, internal, 2483, 2593
-recovered Augustus_model.g40571.t1, internal, 2804, 2955
-recovered Augustus_model.g40571.t1, internal, 3092, 3272
-recovered Augustus_model.g40571.t1, internal, 3645, 3746
-recovered Augustus_model.g40571.t1, internal, 3866, 3964
Valid prediction for snap_scaffold_37-snap.8-T1
Valid prediction for GeneMark_model.106194_t
Valid prediction for snap_scaffold_37-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_60993-T1
Valid prediction for GlimmerHMM_glimmerT_60990-T1
Valid prediction for GeneMark_model.106192_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for Augustus_model.g40574.t1
Couldn't classify 13881, 13958
Sorry, prediction pasa_asmbl_41012.p2 fails validation.
(AGA)	 GC	13881-13958	GT	AGG
(GAT)	 AG	14598-15076	GT	AGG
(CTC)	 AG	15243-15329	GT	ACG
(GCG)	 AG	15436-15538	GT	AGG
(GCC)	 AG	15697-15729	GC	GAG
-recovered pasa_asmbl_41012.p2, terminal, 15697, 15729
-recovered pasa_asmbl_41012.p2, internal, 14598, 15076
-recovered pasa_asmbl_41012.p2, internal, 15243, 15329
-recovered pasa_asmbl_41012.p2, internal, 15436, 15538
-recovered pasa_asmbl_41012.p2, internal, 15697, 15729
Valid prediction for snap_scaffold_37-snap.4-T1
Valid prediction for GeneMark_model.106189_t
Couldn't classify 38410, 38500
Sorry, prediction GeneMark_model.106188_t fails validation.
(ATG)	 AC	37937-37950	GT	GAG
(CTT)	 AG	38086-38100	GT	GAG
(ACT)	 AG	38122-38388	GT	CAG
(ACT)	 AG	38410-38500	GT	TAG
-recovered GeneMark_model.106188_t, initial, 37937, 37950
-recovered GeneMark_model.106188_t, internal, 38086, 38100
-recovered GeneMark_model.106188_t, internal, 38122, 38388
-recovered GeneMark_model.106188_t, internal, 38410, 38500
Valid prediction for snap_scaffold_37-snap.10-T1
Valid prediction for Augustus_model.g40575.t1
Valid prediction for snap_scaffold_37-snap.9-T1
Valid prediction for GeneMark_model.106191_t
Valid prediction for GeneMark_model.106193_t
Valid prediction for Augustus_model.g40572.t1
Valid prediction for GeneMark_model.106195_t
Valid prediction for GlimmerHMM_glimmerT_60991-T1
Valid prediction for GlimmerHMM_glimmerT_60992-T1
Valid prediction for snap_scaffold_37-snap.7-T1
Couldn't classify 38393, 38500
Sorry, prediction snap_scaffold_37-snap.1-T1 fails validation.
(ATG)	 AG	37028-37350	GT	TGG
(TCA)	 AG	38012-38168	GT	CAG
(GAG)	 AG	38393-38500	GT	TAG
-recovered snap_scaffold_37-snap.1-T1, initial, 37028, 37350
-recovered snap_scaffold_37-snap.1-T1, internal, 37028, 37350
-recovered snap_scaffold_37-snap.1-T1, internal, 38012, 38168
-recovered snap_scaffold_37-snap.1-T1, internal, 38393, 38500

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 1487, rend_intergenic: 455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25585, rend_intergenic: 22947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26785, rend_intergenic: 26258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29665, rend_intergenic: 27002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 38514
-exon list size: 133


building trellis

0.7    
1.5    
2.2    
3.0    
3.7    
4.4    
5.2    
5.9    
6.7    
7.4    
8.1    
8.9    
9.6    
10.4    
11.1    
11.9    
12.6    
13.3    
14.1    
14.8    
15.6    
16.3    
17.0    
17.8    
18.5    
19.3    
20.0    
20.7    
21.5    
22.2    
23.0    
23.7    
24.4    
25.2    
25.9    
26.7    
27.4    
28.1    
28.9    
29.6    
30.4    
31.1    
31.9    
32.6    
33.3    
34.1    
34.8    
35.6    
36.3    
37.0    
37.8    
38.5    
39.3    
40.0    
40.7    
41.5    
42.2    
43.0    
43.7    
44.4    
45.2    
45.9    
46.7    
47.4    
48.1    
48.9    
49.6    
50.4    
51.1    
51.9    
52.6    
53.3    
54.1    
54.8    
55.6    
56.3    
57.0    
57.8    
58.5    
59.3    
60.0    
60.7    
61.5    
62.2    
63.0    
63.7    
64.4    
65.2    
65.9    
66.7    
67.4    
68.1    
68.9    
69.6    
70.4    
71.1    
71.9    
72.6    
73.3    
74.1    
74.8    
75.6    
76.3    
77.0    
77.8    
78.5    
79.3    
80.0    
80.7    
81.5    
82.2    
83.0    
83.7    
84.4    
85.2    
85.9    
86.7    
87.4    
88.1    
88.9    
89.6    
90.4    
91.1    
91.9    
92.6    
93.3    
94.1    
94.8    
95.6    
96.3    
97.0    
97.8    
98.5    
99.3    
-found 7 predictions from path traversal
Error with prediction: snap lend_intergenic: 1487, rend_intergenic: 455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25585, rend_intergenic: 22947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26785, rend_intergenic: 26258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29665, rend_intergenic: 27002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 6 predictions persist after filtering for low support