-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_85

-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 Augustus_model.g40735.t1
Couldn't classify 17742, 17872
Sorry, prediction snap_scaffold_85-snap.2-T1 fails validation.
(ATG)	 AC	7990-8144	GT	TGG
(GTG)	 AG	9663-9726	GT	CCG
(GTG)	 AG	13027-13163	GT	AGG
(GTT)	 AG	14084-14192	GT	ACG
(GCT)	 AG	14566-14674	GT	AGG
(AAG)	 AG	14996-15135	GT	GGG
(GTG)	 AG	15226-15343	GT	AGG
(TAG)	 AG	16620-16781	GT	AGG
(CTC)	 AG	17261-17347	GT	GTG
(CGG)	 AG	17742-17872	GT	AGG
-recovered snap_scaffold_85-snap.2-T1, initial, 7990, 8144
-recovered snap_scaffold_85-snap.2-T1, internal, 9663, 9726
-recovered snap_scaffold_85-snap.2-T1, internal, 13027, 13163
-recovered snap_scaffold_85-snap.2-T1, internal, 14084, 14192
-recovered snap_scaffold_85-snap.2-T1, internal, 14566, 14674
-recovered snap_scaffold_85-snap.2-T1, internal, 14996, 15135
-recovered snap_scaffold_85-snap.2-T1, internal, 15226, 15343
-recovered snap_scaffold_85-snap.2-T1, internal, 16620, 16781
-recovered snap_scaffold_85-snap.2-T1, internal, 17261, 17347
-recovered snap_scaffold_85-snap.2-T1, internal, 17742, 17872
Couldn't classify 17742, 17872
Sorry, prediction GlimmerHMM_glimmerT_61240-T1 fails validation.
(ATG)	 AC	13060-13262	GT	AGG
(GTT)	 AG	14084-14192	GT	ACG
(GCT)	 AG	14566-14674	GT	AGG
(AAG)	 AG	14996-15090	GT	TGG
(GTG)	 AG	15226-15343	GT	AGG
(TAG)	 AG	16620-16781	GT	AGG
(CGG)	 AG	17742-17872	GT	AGG
-recovered GlimmerHMM_glimmerT_61240-T1, initial, 13060, 13262
-recovered GlimmerHMM_glimmerT_61240-T1, internal, 14084, 14192
-recovered GlimmerHMM_glimmerT_61240-T1, internal, 14566, 14674
-recovered GlimmerHMM_glimmerT_61240-T1, internal, 14996, 15090
-recovered GlimmerHMM_glimmerT_61240-T1, internal, 15226, 15343
-recovered GlimmerHMM_glimmerT_61240-T1, internal, 16620, 16781
-recovered GlimmerHMM_glimmerT_61240-T1, internal, 17742, 17872
Valid prediction for GeneMark_model.106478_t
Valid prediction for GeneMark_model.106475_t
Valid prediction for GeneMark_model.106480_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: -)Couldn't classify 14463, 14509
Couldn't classify 18323, 18354
Sorry, prediction pasa_asmbl_53689.p1 fails validation.
(CCT)	 AG	14463-14509	GT	AGG
(CAG)	 AG	14681-14874	GT	TGG
(ACA)	 AG	15075-15257	GT	TGG
(GTG)	 AG	15690-15938	GT	TGG
(ATG)	 AG	16067-16185	GT	AGG
(TTT)	 AG	16279-16386	GT	TGG
(ATC)	 AG	16582-16756	GT	CTG
(TCC)	 AG	16869-17007	GT	TGG
(GAA)	 AG	17102-17205	GT	CGG
(GAT)	 AG	17307-17395	GT	AGG
(GTT)	 AG	17499-17652	GT	TGG
(GCA)	 AG	17740-17903	GT	AGG
(GCC)	 AG	17997-18090	GT	GAG
(CTG)	 AG	18323-18354	GA	CGG
add_exon() Sorry, pasa_asmbl_53689.p1 16067-16185-initial-1 is invalid.
-recovered pasa_asmbl_53689.p1, initial, 16067, 16185
-recovered pasa_asmbl_53689.p1, internal, 14463, 14509
-recovered pasa_asmbl_53689.p1, internal, 14681, 14874
-recovered pasa_asmbl_53689.p1, internal, 15075, 15257
-recovered pasa_asmbl_53689.p1, internal, 15690, 15938
-recovered pasa_asmbl_53689.p1, internal, 16067, 16185
-recovered pasa_asmbl_53689.p1, internal, 16279, 16386
-recovered pasa_asmbl_53689.p1, internal, 16582, 16756
-recovered pasa_asmbl_53689.p1, internal, 16869, 17007
-recovered pasa_asmbl_53689.p1, internal, 17102, 17205
-recovered pasa_asmbl_53689.p1, internal, 17307, 17395
-recovered pasa_asmbl_53689.p1, internal, 17499, 17652
-recovered pasa_asmbl_53689.p1, internal, 17740, 17903
-recovered pasa_asmbl_53689.p1, internal, 17997, 18090
Couldn't classify 672, 870
Sorry, prediction snap_scaffold_85-snap.5-T1 fails validation.
(GAG)	 AG	672-870	GT	ATG
(CTC)	 AG	943-1006	GT	GTG
(GGG)	 AG	1068-1215	GT	GGG
(GGC)	 AG	1311-1449	GT	CAG
(CCC)	 AG	1638-1847	GA	AGG
-recovered snap_scaffold_85-snap.5-T1, terminal, 1638, 1847
-recovered snap_scaffold_85-snap.5-T1, internal, 672, 870
-recovered snap_scaffold_85-snap.5-T1, internal, 943, 1006
-recovered snap_scaffold_85-snap.5-T1, internal, 1068, 1215
-recovered snap_scaffold_85-snap.5-T1, internal, 1311, 1449
Valid prediction for GeneMark_model.106477_t
Couldn't classify 52, 60
Sorry, prediction GeneMark_model.106481_t fails validation.
(TGA)	 AG	52-60	GT	CAG
(AGC)	 AG	82-90	GT	CAG
(AGA)	 AG	115-135	GT	CAG
(AGA)	 AG	157-195	GT	GAG
(ACA)	 AG	227-388	GC	AGG
(ATA)	 AG	411-536	GT	GAG
(GAG)	 AG	693-870	GT	ATG
(CTC)	 AG	943-1004	GT	CAG
(GGG)	 AG	1117-1215	GT	GGG
(GGC)	 AG	1311-1449	GT	CAG
(GTG)	 AG	1650-1843	GT	GGG
(GAG)	 AG	1877-1894	GT	TGG
(GGT)	 AG	1918-1947	GT	AGG
(GGA)	 AG	1972-2092	GT	TGG
(TGT)	 AG	2973-2982	GT	TGG
(CGT)	 AG	3065-3202	GT	CAG
(CCT)	 AG	3308-3413	GT	GTG
(AGG)	 AG	3440-3515	GT	AAG
(TAC)	 AG	3641-3646	CA	GAC
-recovered GeneMark_model.106481_t, terminal, 3641, 3646
-recovered GeneMark_model.106481_t, internal, 52, 60
-recovered GeneMark_model.106481_t, internal, 82, 90
-recovered GeneMark_model.106481_t, internal, 115, 135
-recovered GeneMark_model.106481_t, internal, 157, 195
-recovered GeneMark_model.106481_t, internal, 227, 388
-recovered GeneMark_model.106481_t, internal, 411, 536
-recovered GeneMark_model.106481_t, internal, 693, 870
-recovered GeneMark_model.106481_t, internal, 943, 1004
-recovered GeneMark_model.106481_t, internal, 1117, 1215
-recovered GeneMark_model.106481_t, internal, 1311, 1449
-recovered GeneMark_model.106481_t, internal, 1650, 1843
-recovered GeneMark_model.106481_t, internal, 1877, 1894
-recovered GeneMark_model.106481_t, internal, 1918, 1947
-recovered GeneMark_model.106481_t, internal, 1972, 2092
-recovered GeneMark_model.106481_t, internal, 2973, 2982
-recovered GeneMark_model.106481_t, internal, 3065, 3202
-recovered GeneMark_model.106481_t, internal, 3308, 3413
-recovered GeneMark_model.106481_t, internal, 3440, 3515
Valid prediction for snap_scaffold_85-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_61239-T1
Valid prediction for snap_scaffold_85-snap.3-T1
Couldn't classify 18323, 18402
Sorry, prediction HiQ_model.g40733.t1 fails validation.
(ATG)	 AA	14274-14509	GT	AGG
(CAG)	 AG	14681-14874	GT	TGG
(ACA)	 AG	15075-15257	GT	TGG
(GTG)	 AG	15690-15938	GT	TGG
(ATG)	 AG	16067-16185	GT	AGG
(TTT)	 AG	16279-16386	GT	TGG
(ATC)	 AG	16582-16756	GT	CTG
(TCC)	 AG	16869-17007	GT	TGG
(GAA)	 AG	17102-17205	GT	CGG
(GAT)	 AG	17307-17395	GT	AGG
(GTT)	 AG	17499-17652	GT	TGG
(GCA)	 AG	17740-17903	GT	AGG
(GCC)	 AG	17997-18090	GT	GAG
(CTG)	 AG	18323-18402		TG
-recovered HiQ_model.g40733.t1, initial, 14274, 14509
add_exon() Sorry, HiQ_model.g40733.t1 16067-16185-initial-1 is invalid.
-recovered HiQ_model.g40733.t1, initial, 16067, 16185
-recovered HiQ_model.g40733.t1, internal, 14681, 14874
-recovered HiQ_model.g40733.t1, internal, 15075, 15257
-recovered HiQ_model.g40733.t1, internal, 15690, 15938
-recovered HiQ_model.g40733.t1, internal, 16067, 16185
-recovered HiQ_model.g40733.t1, internal, 16279, 16386
-recovered HiQ_model.g40733.t1, internal, 16582, 16756
-recovered HiQ_model.g40733.t1, internal, 16869, 17007
-recovered HiQ_model.g40733.t1, internal, 17102, 17205
-recovered HiQ_model.g40733.t1, internal, 17307, 17395
-recovered HiQ_model.g40733.t1, internal, 17499, 17652
-recovered HiQ_model.g40733.t1, internal, 17740, 17903
-recovered HiQ_model.g40733.t1, internal, 17997, 18090
Valid prediction for GeneMark_model.106476_t
Valid prediction for GeneMark_model.106479_t
Valid prediction for GlimmerHMM_glimmerT_61237-T1
Valid prediction for GlimmerHMM_glimmerT_61238-T1
Couldn't classify 17997, 18090
Sorry, prediction snap_scaffold_85-snap.1-T1 fails validation.
(ATG)	 AA	14274-14378	GT	GTG
(ATC)	 AG	14448-14509	GT	AGG
(TGT)	 AG	14684-14874	GT	TGG
(ACA)	 AG	15075-15257	GT	TGG
(GTG)	 AG	15690-15938	GT	TGG
(ATG)	 AG	16067-16185	GT	AGG
(TTT)	 AG	16279-16386	GT	TGG
(ATC)	 AG	16582-16756	GT	CTG
(TCC)	 AG	16869-17007	GT	TGG
(GAA)	 AG	17102-17205	GT	CGG
(GAT)	 AG	17307-17395	GT	AGG
(GTT)	 AG	17499-17652	GT	TGG
(GCA)	 AG	17740-17903	GT	AGG
(GCC)	 AG	17997-18090	GT	GAG
-recovered snap_scaffold_85-snap.1-T1, initial, 14274, 14378
add_exon() Sorry, snap_scaffold_85-snap.1-T1 16067-16185-initial-1 is invalid.
-recovered snap_scaffold_85-snap.1-T1, initial, 16067, 16185
-recovered snap_scaffold_85-snap.1-T1, internal, 14448, 14509
-recovered snap_scaffold_85-snap.1-T1, internal, 14684, 14874
-recovered snap_scaffold_85-snap.1-T1, internal, 15075, 15257
-recovered snap_scaffold_85-snap.1-T1, internal, 15690, 15938
-recovered snap_scaffold_85-snap.1-T1, internal, 16067, 16185
-recovered snap_scaffold_85-snap.1-T1, internal, 16279, 16386
-recovered snap_scaffold_85-snap.1-T1, internal, 16582, 16756
-recovered snap_scaffold_85-snap.1-T1, internal, 16869, 17007
-recovered snap_scaffold_85-snap.1-T1, internal, 17102, 17205
-recovered snap_scaffold_85-snap.1-T1, internal, 17307, 17395
-recovered snap_scaffold_85-snap.1-T1, internal, 17499, 17652
-recovered snap_scaffold_85-snap.1-T1, internal, 17740, 17903
-recovered snap_scaffold_85-snap.1-T1, internal, 17997, 18090
Valid prediction for Augustus_model.g40734.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17872, rend_intergenic: 11327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 18402
-exon list size: 128


building trellis

0.8    
1.5    
2.3    
3.1    
3.8    
4.6    
5.4    
6.2    
6.9    
7.7    
8.5    
9.2    
10.0    
10.8    
11.5    
12.3    
13.1    
13.8    
14.6    
15.4    
16.2    
16.9    
17.7    
18.5    
19.2    
20.0    
20.8    
21.5    
22.3    
23.1    
23.8    
24.6    
25.4    
26.2    
26.9    
27.7    
28.5    
29.2    
30.0    
30.8    
31.5    
32.3    
33.1    
33.8    
34.6    
35.4    
36.2    
36.9    
37.7    
38.5    
39.2    
40.0    
40.8    
41.5    
42.3    
43.1    
43.8    
44.6    
45.4    
46.2    
46.9    
47.7    
48.5    
49.2    
50.0    
50.8    
51.5    
52.3    
53.1    
53.8    
54.6    
55.4    
56.2    
56.9    
57.7    
58.5    
59.2    
60.0    
60.8    
61.5    
62.3    
63.1    
63.8    
64.6    
65.4    
66.2    
66.9    
67.7    
68.5    
69.2    
70.0    
70.8    
71.5    
72.3    
73.1    
73.8    
74.6    
75.4    
76.2    
76.9    
77.7    
78.5    
79.2    
80.0    
80.8    
81.5    
82.3    
83.1    
83.8    
84.6    
85.4    
86.2    
86.9    
87.7    
88.5    
89.2    
90.0    
90.8    
91.5    
92.3    
93.1    
93.8    
94.6    
95.4    
96.2    
96.9    
97.7    
98.5    
99.2    
-found 4 predictions from path traversal
Error with prediction: snap lend_intergenic: 17872, rend_intergenic: 11327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support