-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_524

-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: +)Couldn't classify 1494, 1600
Couldn't classify 5157, 5248
Sorry, prediction snap_scaffold_524-snap.2-T1 fails validation.
(AGG)	 AG	1494-1600	GT	GAG
(ATG)	 AG	1890-1910	GT	AGG
(ACC)	 AG	1952-2050	GT	AAG
(GGT)	 AG	3550-3657	GT	CGG
(AGG)	 AG	5157-5248	GT	CTG
-recovered snap_scaffold_524-snap.2-T1, initial, 1890, 1910
-recovered snap_scaffold_524-snap.2-T1, internal, 1494, 1600
-recovered snap_scaffold_524-snap.2-T1, internal, 1890, 1910
-recovered snap_scaffold_524-snap.2-T1, internal, 1952, 2050
-recovered snap_scaffold_524-snap.2-T1, internal, 3550, 3657
-recovered snap_scaffold_524-snap.2-T1, internal, 5157, 5248
Couldn't classify 5708, 5775
Sorry, prediction GeneMark_model.107858_t fails validation.
(ATG)	 AC	3840-3883	GT	GTG
(AAG)	 AG	3923-4087	GT	GAG
(AGA)	 AG	4119-4253	GC	GGG
(AGA)	 AG	4278-4374	GT	GAG
(ACA)	 AG	4812-4831	GT	AAG
(GAA)	 AG	5159-5248	GT	CTG
(GCC)	 AG	5292-5337	GT	GGG
(ACA)	 AG	5427-5437	GT	AGG
(TGA)	 AG	5708-5775	GT	AGG
-recovered GeneMark_model.107858_t, initial, 3840, 3883
-recovered GeneMark_model.107858_t, internal, 3923, 4087
-recovered GeneMark_model.107858_t, internal, 4119, 4253
-recovered GeneMark_model.107858_t, internal, 4278, 4374
-recovered GeneMark_model.107858_t, internal, 4812, 4831
-recovered GeneMark_model.107858_t, internal, 5159, 5248
-recovered GeneMark_model.107858_t, internal, 5292, 5337
-recovered GeneMark_model.107858_t, internal, 5427, 5437
-recovered GeneMark_model.107858_t, internal, 5708, 5775

-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 261, 425
Couldn't classify 5679, 5825
Sorry, prediction Augustus_model.g41179.t1 fails validation.
(GGC)	 AG	261-425	GT	CAG
(GTT)	 AG	641-707	GT	AGG
(TGT)	 AG	812-997	GT	CGG
(GTA)	 AG	1262-1348	GT	AGG
(GTG)	 AG	1646-1738	GT	GGG
(CCT)	 AG	2289-2342	GT	AGG
(GCG)	 AG	2439-2589	GT	AGG
(ATG)	 AG	2852-2988	GT	AGG
(GAG)	 AG	3893-3970	GT	AGG
(TTT)	 AG	4108-4253	GT	AGG
(TGC)	 AG	4535-4652	GT	AGG
(GCT)	 AG	4806-5028	GT	AGG
(GTG)	 AG	5296-5444	GT	AGG
(GAG)	 AG	5679-5825	GT	AGG
add_exon() Sorry, Augustus_model.g41179.t1 2852-2988-initial-1 is invalid.
-recovered Augustus_model.g41179.t1, initial, 2852, 2988
-recovered Augustus_model.g41179.t1, internal, 261, 425
-recovered Augustus_model.g41179.t1, internal, 641, 707
-recovered Augustus_model.g41179.t1, internal, 812, 997
-recovered Augustus_model.g41179.t1, internal, 1262, 1348
-recovered Augustus_model.g41179.t1, internal, 1646, 1738
-recovered Augustus_model.g41179.t1, internal, 2289, 2342
-recovered Augustus_model.g41179.t1, internal, 2439, 2589
-recovered Augustus_model.g41179.t1, internal, 2852, 2988
-recovered Augustus_model.g41179.t1, internal, 3893, 3970
-recovered Augustus_model.g41179.t1, internal, 4108, 4253
-recovered Augustus_model.g41179.t1, internal, 4535, 4652
-recovered Augustus_model.g41179.t1, internal, 4806, 5028
-recovered Augustus_model.g41179.t1, internal, 5296, 5444
-recovered Augustus_model.g41179.t1, internal, 5679, 5825
Couldn't classify 261, 425
Sorry, prediction GlimmerHMM_glimmerT_61953-T1 fails validation.
(GGC)	 AG	261-425	GT	CAG
(GTT)	 AG	641-707	GT	AGG
(TGT)	 AG	812-997	GT	CGG
(GTG)	 AG	1646-1738	GT	GGG
(CCT)	 AG	2289-2342	GT	AGG
(GCG)	 AG	2439-2589	GT	AGG
(ATG)	 AG	2852-2988	GT	AGG
(TTT)	 AG	4108-4257	GA	AGG
add_exon() Sorry, GlimmerHMM_glimmerT_61953-T1 2852-2988-initial-1 is invalid.
-recovered GlimmerHMM_glimmerT_61953-T1, initial, 2852, 2988
-recovered GlimmerHMM_glimmerT_61953-T1, terminal, 4108, 4257
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 261, 425
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 641, 707
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 812, 997
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 1646, 1738
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 2289, 2342
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 2439, 2589
-recovered GlimmerHMM_glimmerT_61953-T1, internal, 2852, 2988
Couldn't classify 5679, 5825
Sorry, prediction GeneMark_model.107857_t fails validation.
(ATG)	 TC	2409-2417	GT	CTG
(GCG)	 AG	2439-2589	GT	AGG
(TCC)	 AG	2616-2731	GT	CTG
(ACC)	 AG	2758-2831	GT	TTG
(GAG)	 AG	2865-2988	GT	AGG
(GGA)	 AG	3065-3135	GT	AGG
(CTT)	 AG	3208-3276	GT	GGG
(CTG)	 AG	3303-3425	GT	AGG
(CTG)	 AG	3462-3509	GT	AGG
(GAG)	 AG	3536-3541	GT	AGG
(CTG)	 AG	3590-3601	GT	GAG
(CTG)	 AG	3622-3633	GT	GAG
(CTG)	 AG	3654-3665	GT	GAG
(GAT)	 AG	3710-3793	GT	GGG
(CTG)	 AG	3820-3831	GT	GAG
(GAG)	 AG	3862-3888	GT	GGG
(GAG)	 AG	3913-3970	GT	AGG
(TTT)	 AG	4108-4253	GT	AGG
(TCA)	 AG	4278-4286	GT	GTG
(GGG)	 AG	4309-4318	GT	GAG
(GGG)	 AG	4345-4358	GT	GTG
(GGG)	 AG	4381-4392	GT	GTG
(AGG)	 AG	4417-4446	GT	GTG
(GGG)	 AG	4471-4482	GT	GTG
(TGC)	 AG	4535-4652	GT	AGG
(GCT)	 AG	4806-5041	GT	AGG
(GGC)	 AG	5291-5444	GT	AGG
(GAG)	 AG	5679-5825	GT	AGG
-recovered GeneMark_model.107857_t, initial, 2409, 2417
-recovered GeneMark_model.107857_t, terminal, 3462, 3509
-recovered GeneMark_model.107857_t, internal, 2439, 2589
-recovered GeneMark_model.107857_t, internal, 2616, 2731
-recovered GeneMark_model.107857_t, internal, 2758, 2831
-recovered GeneMark_model.107857_t, internal, 2865, 2988
-recovered GeneMark_model.107857_t, internal, 3065, 3135
-recovered GeneMark_model.107857_t, internal, 3208, 3276
-recovered GeneMark_model.107857_t, internal, 3303, 3425
-recovered GeneMark_model.107857_t, internal, 3462, 3509
-recovered GeneMark_model.107857_t, internal, 3536, 3541
-recovered GeneMark_model.107857_t, internal, 3590, 3601
-recovered GeneMark_model.107857_t, internal, 3622, 3633
-recovered GeneMark_model.107857_t, internal, 3654, 3665
-recovered GeneMark_model.107857_t, internal, 3710, 3793
-recovered GeneMark_model.107857_t, internal, 3820, 3831
-recovered GeneMark_model.107857_t, internal, 3862, 3888
-recovered GeneMark_model.107857_t, internal, 3913, 3970
-recovered GeneMark_model.107857_t, internal, 4108, 4253
-recovered GeneMark_model.107857_t, internal, 4278, 4286
-recovered GeneMark_model.107857_t, internal, 4309, 4318
-recovered GeneMark_model.107857_t, internal, 4345, 4358
-recovered GeneMark_model.107857_t, internal, 4381, 4392
-recovered GeneMark_model.107857_t, internal, 4417, 4446
-recovered GeneMark_model.107857_t, internal, 4471, 4482
-recovered GeneMark_model.107857_t, internal, 4535, 4652
-recovered GeneMark_model.107857_t, internal, 4806, 5041
-recovered GeneMark_model.107857_t, internal, 5291, 5444
-recovered GeneMark_model.107857_t, internal, 5679, 5825
Couldn't classify 261, 425
Couldn't classify 5745, 5825
Sorry, prediction snap_scaffold_524-snap.1-T1 fails validation.
(GGC)	 AG	261-425	GT	CAG
(GTT)	 AG	641-707	GT	AGG
(TGT)	 AG	812-997	GT	CGG
(GTA)	 AG	1262-1348	GT	AGG
(GTG)	 AG	1646-1738	GT	GGG
(CCT)	 AG	2289-2342	GT	AGG
(GCG)	 AG	2439-2589	GT	AGG
(ATG)	 AG	2852-2988	GT	AGG
(GGA)	 AG	3065-3164	GT	GGG
(GAG)	 AG	3218-3509	GT	AGG
(GAG)	 AG	3913-3970	GT	AGG
(TTT)	 AG	4108-4253	GT	AGG
(TGC)	 AG	4535-4652	GT	AGG
(GCT)	 AG	4806-5028	GT	AGG
(GTG)	 AG	5296-5444	GT	AGG
(GCT)	 AG	5745-5825	GT	AGG
add_exon() Sorry, snap_scaffold_524-snap.1-T1 2852-2988-initial-1 is invalid.
-recovered snap_scaffold_524-snap.1-T1, initial, 2852, 2988
add_exon() Sorry, snap_scaffold_524-snap.1-T1 3218-3509-terminal-3 is invalid.
-recovered snap_scaffold_524-snap.1-T1, terminal, 3218, 3509
-recovered snap_scaffold_524-snap.1-T1, internal, 261, 425
-recovered snap_scaffold_524-snap.1-T1, internal, 641, 707
-recovered snap_scaffold_524-snap.1-T1, internal, 812, 997
-recovered snap_scaffold_524-snap.1-T1, internal, 1262, 1348
-recovered snap_scaffold_524-snap.1-T1, internal, 1646, 1738
-recovered snap_scaffold_524-snap.1-T1, internal, 2289, 2342
-recovered snap_scaffold_524-snap.1-T1, internal, 2439, 2589
-recovered snap_scaffold_524-snap.1-T1, internal, 2852, 2988
-recovered snap_scaffold_524-snap.1-T1, internal, 3065, 3164
-recovered snap_scaffold_524-snap.1-T1, internal, 3218, 3509
-recovered snap_scaffold_524-snap.1-T1, internal, 3913, 3970
-recovered snap_scaffold_524-snap.1-T1, internal, 4108, 4253
-recovered snap_scaffold_524-snap.1-T1, internal, 4535, 4652
-recovered snap_scaffold_524-snap.1-T1, internal, 4806, 5028
-recovered snap_scaffold_524-snap.1-T1, internal, 5296, 5444
-recovered snap_scaffold_524-snap.1-T1, internal, 5745, 5825
Valid prediction for GlimmerHMM_glimmerT_61952-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5856, rend_intergenic: 1494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6116
-exon list size: 117


building trellis

0.8    
1.7    
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3.4    
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5.0    
5.9    
6.7    
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8.4    
9.2    
10.1    
10.9    
11.8    
12.6    
13.4    
14.3    
15.1    
16.0    
16.8    
17.6    
18.5    
19.3    
20.2    
21.0    
21.8    
22.7    
23.5    
24.4    
25.2    
26.1    
26.9    
27.7    
28.6    
29.4    
30.3    
31.1    
31.9    
32.8    
33.6    
34.5    
35.3    
36.1    
37.0    
37.8    
38.7    
39.5    
40.3    
41.2    
42.0    
42.9    
43.7    
44.5    
45.4    
46.2    
47.1    
47.9    
48.7    
49.6    
50.4    
51.3    
52.1    
52.9    
53.8    
54.6    
55.5    
56.3    
57.1    
58.0    
58.8    
59.7    
60.5    
61.3    
62.2    
63.0    
63.9    
64.7    
65.5    
66.4    
67.2    
68.1    
68.9    
69.7    
70.6    
71.4    
72.3    
73.1    
73.9    
74.8    
75.6    
76.5    
77.3    
78.2    
79.0    
79.8    
80.7    
81.5    
82.4    
83.2    
84.0    
84.9    
85.7    
86.6    
87.4    
88.2    
89.1    
89.9    
90.8    
91.6    
92.4    
93.3    
94.1    
95.0    
95.8    
96.6    
97.5    
98.3    
99.2    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5856, rend_intergenic: 1494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support