-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_241

-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 GlimmerHMM_glimmerT_61560-T1
Valid prediction for snap_scaffold_241-snap.4-T1
Couldn't classify 9066, 9113
Sorry, prediction GeneMark_model.107050_t fails validation.
(ATG)	 CT	8672-8703	GT	AGG
(AGG)	 AG	8979-9008	GC	GAG
(AGA)	 AG	9030-9041	GT	AGG
(AGA)	 AG	9066-9113	GT	CTG
-recovered GeneMark_model.107050_t, initial, 8672, 8703
-recovered GeneMark_model.107050_t, internal, 8979, 9008
-recovered GeneMark_model.107050_t, internal, 9030, 9041
-recovered GeneMark_model.107050_t, internal, 9066, 9113
Valid prediction for Augustus_model.g40936.t1
Valid prediction for Augustus_model.g40935.t1
Valid prediction for GeneMark_model.107047_t
Valid prediction for snap_scaffold_241-snap.3-T1

-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 snap_scaffold_241-snap.1-T1
Valid prediction for GeneMark_model.107049_t
Couldn't classify 518, 732
Sorry, prediction Augustus_model.g40937.t1 fails validation.
(GAG)	 AG	518-732	GT	AGG
(AGC)	 AG	1451-1498	AG	AAA
-recovered Augustus_model.g40937.t1, terminal, 1451, 1498
-recovered Augustus_model.g40937.t1, internal, 518, 732
Valid prediction for Augustus_model.g40934.t1
Couldn't classify 9156, 9162
Sorry, prediction GeneMark_model.107046_t fails validation.
(ATG)	 AA	6051-6068	GT	AGG
(GGA)	 AG	6276-6509	GT	AGG
(GTG)	 AG	6893-6999	GT	GAG
(AGA)	 AG	7588-7626	GT	GGG
(GCT)	 AG	7657-7692	GT	GGG
(AGA)	 AG	7716-7724	GT	GGG
(GGT)	 AG	7751-7759	GT	GGG
(AGA)	 AG	7787-7795	GT	GGG
(AGA)	 AG	7818-7826	GT	GGG
(AGA)	 AG	7850-7858	GT	GGG
(AGA)	 AG	7878-7892	GT	GGG
(AGG)	 AG	7914-7922	GT	GGG
(GGG)	 AG	7946-7954	GT	GGG
(AGA)	 AG	7987-7998	GT	AGG
(AGA)	 AG	8034-8042	GT	GGG
(AGA)	 AG	8066-8074	GT	GGG
(GGT)	 AG	8112-8117	GT	AAG
(GGG)	 AG	8142-8150	GT	CGG
(AGA)	 AG	8176-8193	GT	AGG
(AGA)	 AG	8223-8231	GT	GGG
(AGA)	 AG	8257-8268	GT	AGG
(GGG)	 AG	8298-8306	GT	GGG
(AGA)	 AG	8330-8338	GT	GGG
(AAA)	 AG	8367-8375	GT	GGG
(AGG)	 AG	8410-8442	GT	GGG
(AGG)	 AG	8487-8495	GT	GGG
(AGA)	 AG	8521-8532	GT	AGG
(AAA)	 AG	8556-8564	GT	GGG
(AGA)	 AG	8590-8601	GT	AGG
(AGG)	 AG	8631-8657	GT	GGG
(AGA)	 AG	8696-8707	GT	AGG
(AGA)	 AG	8739-8750	GT	AGG
(AGA)	 AG	8780-8788	GT	GGG
(AGA)	 AG	8814-8825	GT	AGG
(AGA)	 AG	8859-8867	GT	GGG
(AGG)	 AG	8897-8905	GT	GGG
(AGA)	 AG	8929-8940	GT	AGG
(AGA)	 AG	8966-8977	GT	AGG
(AGA)	 AG	9009-9017	GT	GGG
(AGA)	 AG	9049-9060	GT	AGG
(AGA)	 AG	9084-9092	GT	GGG
(GGT)	 AG	9122-9130	GT	GGG
(AGA)	 AG	9156-9162	GT	GGG
-recovered GeneMark_model.107046_t, initial, 6051, 6068
-recovered GeneMark_model.107046_t, terminal, 7987, 7998
-recovered GeneMark_model.107046_t, terminal, 8112, 8117
-recovered GeneMark_model.107046_t, terminal, 8176, 8193
-recovered GeneMark_model.107046_t, terminal, 8257, 8268
-recovered GeneMark_model.107046_t, terminal, 8521, 8532
-recovered GeneMark_model.107046_t, terminal, 8590, 8601
-recovered GeneMark_model.107046_t, terminal, 8696, 8707
-recovered GeneMark_model.107046_t, terminal, 8739, 8750
-recovered GeneMark_model.107046_t, terminal, 8814, 8825
-recovered GeneMark_model.107046_t, terminal, 8929, 8940
-recovered GeneMark_model.107046_t, terminal, 8966, 8977
-recovered GeneMark_model.107046_t, terminal, 9049, 9060
-recovered GeneMark_model.107046_t, internal, 6276, 6509
-recovered GeneMark_model.107046_t, internal, 6893, 6999
-recovered GeneMark_model.107046_t, internal, 7588, 7626
-recovered GeneMark_model.107046_t, internal, 7657, 7692
-recovered GeneMark_model.107046_t, internal, 7716, 7724
-recovered GeneMark_model.107046_t, internal, 7751, 7759
-recovered GeneMark_model.107046_t, internal, 7787, 7795
-recovered GeneMark_model.107046_t, internal, 7818, 7826
-recovered GeneMark_model.107046_t, internal, 7850, 7858
-recovered GeneMark_model.107046_t, internal, 7878, 7892
-recovered GeneMark_model.107046_t, internal, 7914, 7922
-recovered GeneMark_model.107046_t, internal, 7946, 7954
-recovered GeneMark_model.107046_t, internal, 7987, 7998
-recovered GeneMark_model.107046_t, internal, 8034, 8042
-recovered GeneMark_model.107046_t, internal, 8066, 8074
-recovered GeneMark_model.107046_t, internal, 8112, 8117
-recovered GeneMark_model.107046_t, internal, 8142, 8150
-recovered GeneMark_model.107046_t, internal, 8176, 8193
-recovered GeneMark_model.107046_t, internal, 8223, 8231
-recovered GeneMark_model.107046_t, internal, 8257, 8268
-recovered GeneMark_model.107046_t, internal, 8298, 8306
-recovered GeneMark_model.107046_t, internal, 8330, 8338
-recovered GeneMark_model.107046_t, internal, 8367, 8375
-recovered GeneMark_model.107046_t, internal, 8410, 8442
-recovered GeneMark_model.107046_t, internal, 8487, 8495
-recovered GeneMark_model.107046_t, internal, 8521, 8532
-recovered GeneMark_model.107046_t, internal, 8556, 8564
-recovered GeneMark_model.107046_t, internal, 8590, 8601
-recovered GeneMark_model.107046_t, internal, 8631, 8657
-recovered GeneMark_model.107046_t, internal, 8696, 8707
-recovered GeneMark_model.107046_t, internal, 8739, 8750
-recovered GeneMark_model.107046_t, internal, 8780, 8788
-recovered GeneMark_model.107046_t, internal, 8814, 8825
-recovered GeneMark_model.107046_t, internal, 8859, 8867
-recovered GeneMark_model.107046_t, internal, 8897, 8905
-recovered GeneMark_model.107046_t, internal, 8929, 8940
-recovered GeneMark_model.107046_t, internal, 8966, 8977
-recovered GeneMark_model.107046_t, internal, 9009, 9017
-recovered GeneMark_model.107046_t, internal, 9049, 9060
-recovered GeneMark_model.107046_t, internal, 9084, 9092
-recovered GeneMark_model.107046_t, internal, 9122, 9130
-recovered GeneMark_model.107046_t, internal, 9156, 9162
Couldn't classify 518, 732
Sorry, prediction snap_scaffold_241-snap.2-T1 fails validation.
(GAG)	 AG	518-732	GT	AGG
(TCA)	 AG	3265-3382	GT	CGG
(GTT)	 AG	3478-3687	GT	AGG
(GAA)	 AG	5671-5816	CA	AGC
-recovered snap_scaffold_241-snap.2-T1, terminal, 5671, 5816
-recovered snap_scaffold_241-snap.2-T1, internal, 518, 732
-recovered snap_scaffold_241-snap.2-T1, internal, 3265, 3382
-recovered snap_scaffold_241-snap.2-T1, internal, 3478, 3687
Valid prediction for GlimmerHMM_glimmerT_61559-T1
Couldn't classify 518, 732
Sorry, prediction GlimmerHMM_glimmerT_61561-T1 fails validation.
(GAG)	 AG	518-732	GT	AGG
(GAG)	 AG	2359-2505	AG	AAA
-recovered GlimmerHMM_glimmerT_61561-T1, terminal, 2359, 2505
-recovered GlimmerHMM_glimmerT_61561-T1, internal, 518, 732

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8669, rend_intergenic: 3455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9186
-exon list size: 165


building trellis

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1.2    
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2.4    
3.0    
3.6    
4.2    
4.8    
5.4    
6.0    
6.6    
7.2    
7.8    
8.4    
9.0    
9.6    
10.2    
10.8    
11.4    
12.0    
12.6    
13.2    
13.8    
14.4    
15.0    
15.6    
16.2    
16.8    
17.4    
18.0    
18.6    
19.2    
19.8    
20.4    
21.0    
21.6    
22.2    
22.8    
23.4    
24.0    
24.6    
25.1    
25.7    
26.3    
26.9    
27.5    
28.1    
28.7    
29.3    
29.9    
30.5    
31.1    
31.7    
32.3    
32.9    
33.5    
34.1    
34.7    
35.3    
35.9    
36.5    
37.1    
37.7    
38.3    
38.9    
39.5    
40.1    
40.7    
41.3    
41.9    
42.5    
43.1    
43.7    
44.3    
44.9    
45.5    
46.1    
46.7    
47.3    
47.9    
48.5    
49.1    
49.7    
50.3    
50.9    
51.5    
52.1    
52.7    
53.3    
53.9    
54.5    
55.1    
55.7    
56.3    
56.9    
57.5    
58.1    
58.7    
59.3    
59.9    
60.5    
61.1    
61.7    
62.3    
62.9    
63.5    
64.1    
64.7    
65.3    
65.9    
66.5    
67.1    
67.7    
68.3    
68.9    
69.5    
70.1    
70.7    
71.3    
71.9    
72.5    
73.1    
73.7    
74.3    
74.9    
75.4    
76.0    
76.6    
77.2    
77.8    
78.4    
79.0    
79.6    
80.2    
80.8    
81.4    
82.0    
82.6    
83.2    
83.8    
84.4    
85.0    
85.6    
86.2    
86.8    
87.4    
88.0    
88.6    
89.2    
89.8    
90.4    
91.0    
91.6    
92.2    
92.8    
93.4    
94.0    
94.6    
95.2    
95.8    
96.4    
97.0    
97.6    
98.2    
98.8    
99.4    
-found 5 predictions from path traversal
Error with prediction: snap lend_intergenic: 8669, rend_intergenic: 3455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support