-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_143

-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 12471, 12605
Sorry, prediction GlimmerHMM_glimmerT_61378-T1 fails validation.
(ATG)	 GG	3772-3780	GT	AGG
(AAC)	 AG	7202-7282	GT	ATG
(GTG)	 AG	7456-7551	GT	CTG
(ACG)	 AG	11856-12008	GT	CTG
(GGC)	 AG	12471-12605	GT	AGG
-recovered GlimmerHMM_glimmerT_61378-T1, initial, 3772, 3780
-recovered GlimmerHMM_glimmerT_61378-T1, internal, 7202, 7282
-recovered GlimmerHMM_glimmerT_61378-T1, internal, 7456, 7551
-recovered GlimmerHMM_glimmerT_61378-T1, internal, 11856, 12008
-recovered GlimmerHMM_glimmerT_61378-T1, internal, 12471, 12605
Valid prediction for GlimmerHMM_glimmerT_61377-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61377-T1 3013-3199-terminal-1 is invalid.
Valid prediction for snap_scaffold_143-snap.2-T1
Couldn't classify 12471, 12605
Sorry, prediction Augustus_model.g40823.t1 fails validation.
(ATG)	 AC	7118-7282	GT	ATG
(GTG)	 AG	7456-7551	GT	CTG
(ACG)	 AG	11856-12008	GT	CTG
(GGC)	 AG	12471-12605	GT	AGG
-recovered Augustus_model.g40823.t1, initial, 7118, 7282
-recovered Augustus_model.g40823.t1, internal, 7456, 7551
-recovered Augustus_model.g40823.t1, internal, 11856, 12008
-recovered Augustus_model.g40823.t1, internal, 12471, 12605
Valid prediction for Augustus_model.g40822.t1
Valid prediction for snap_scaffold_143-snap.1-T1
Couldn't classify 113, 325
Sorry, prediction GeneMark_model.106722_t fails validation.
(TGA)	 AG	113-325	GT	GGG
(AAA)	 AG	365-400	GT	AGG
(GAA)	 AG	429-440	GC	AGG
(GAA)	 AG	469-480	GC	AGG
(GGA)	 AG	509-514	GC	AGG
(GCA)	 AG	577-627	GT	GAG
(AGA)	 AG	651-935	GT	GGG
(AGG)	 AG	969-1013	GT	GAG
(AGG)	 AG	1037-1075	GC	GGG
(GGG)	 AG	1103-1183	GT	GAG
(AGA)	 AG	1266-1355	GT	GGG
(AGA)	 AG	1405-1506	GC	GCG
(CAG)	 AG	1527-1577	GT	GTG
(AGA)	 AG	1601-1747	GT	GAG
(AAA)	 AG	1774-1840	GT	AGG
(GTG)	 AG	2028-2071	GT	GGG
(GTG)	 AG	2585-2594	GT	AGG
(GCT)	 AG	2711-2787	GT	AGG
(GAA)	 AG	3013-3157	GT	AGG
(GTT)	 AG	3269-3279	GT	GCG
(GGG)	 AG	3326-3568	GT	AGG
(AGA)	 AG	3606-3641	GT	GGG
(GGA)	 AG	3669-3740	GT	GTG
(ATT)	 AG	3762-3780	GT	AGG
(CGC)	 AG	3829-3840	AG	AGA
add_exon() Sorry, GeneMark_model.106722_t 2711-2787-terminal-2 is invalid.
-recovered GeneMark_model.106722_t, terminal, 2711, 2787
-recovered GeneMark_model.106722_t, terminal, 3829, 3840
-recovered GeneMark_model.106722_t, internal, 113, 325
-recovered GeneMark_model.106722_t, internal, 365, 400
-recovered GeneMark_model.106722_t, internal, 429, 440
-recovered GeneMark_model.106722_t, internal, 469, 480
-recovered GeneMark_model.106722_t, internal, 509, 514
-recovered GeneMark_model.106722_t, internal, 577, 627
-recovered GeneMark_model.106722_t, internal, 651, 935
-recovered GeneMark_model.106722_t, internal, 969, 1013
-recovered GeneMark_model.106722_t, internal, 1037, 1075
-recovered GeneMark_model.106722_t, internal, 1103, 1183
-recovered GeneMark_model.106722_t, internal, 1266, 1355
-recovered GeneMark_model.106722_t, internal, 1405, 1506
-recovered GeneMark_model.106722_t, internal, 1527, 1577
-recovered GeneMark_model.106722_t, internal, 1601, 1747
-recovered GeneMark_model.106722_t, internal, 1774, 1840
-recovered GeneMark_model.106722_t, internal, 2028, 2071
-recovered GeneMark_model.106722_t, internal, 2585, 2594
-recovered GeneMark_model.106722_t, internal, 2711, 2787
-recovered GeneMark_model.106722_t, internal, 3013, 3157
-recovered GeneMark_model.106722_t, internal, 3269, 3279
-recovered GeneMark_model.106722_t, internal, 3326, 3568
-recovered GeneMark_model.106722_t, internal, 3606, 3641
-recovered GeneMark_model.106722_t, internal, 3669, 3740
-recovered GeneMark_model.106722_t, internal, 3762, 3780

-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 30, 35
Sorry, prediction GeneMark_model.106723_t fails validation.
(CAT)	 AG	30-35	GT	GGG
(AGG)	 AG	60-104	GT	ATG
(AGT)	 AG	200-271	GT	CTG
(CTC)	 AG	737-923	GT	GCG
(AAG)	 AG	978-1060	GT	AAG
(CAC)	 AG	3932-3966	GT	GAG
(CTC)	 AG	4255-4345	GT	AGG
(GGC)	 AG	4571-4615	GT	TGG
(GGT)	 AG	4657-4710	GT	GTG
(GTT)	 AG	4738-5013	GT	GTG
(GAG)	 AG	5040-5183	GT	GAG
(CGG)	 AG	5247-5286	GT	TGG
(GCC)	 AG	5530-5642	GT	ATG
(ACA)	 AG	8049-8090	GT	ACG
(AGA)	 AG	8449-8484	GT	GAG
(ACC)	 AG	8604-8679	AC	GAA
-recovered GeneMark_model.106723_t, terminal, 4255, 4345
-recovered GeneMark_model.106723_t, terminal, 8449, 8484
-recovered GeneMark_model.106723_t, terminal, 8604, 8679
-recovered GeneMark_model.106723_t, internal, 30, 35
-recovered GeneMark_model.106723_t, internal, 60, 104
-recovered GeneMark_model.106723_t, internal, 200, 271
-recovered GeneMark_model.106723_t, internal, 737, 923
-recovered GeneMark_model.106723_t, internal, 978, 1060
-recovered GeneMark_model.106723_t, internal, 3932, 3966
-recovered GeneMark_model.106723_t, internal, 4255, 4345
-recovered GeneMark_model.106723_t, internal, 4571, 4615
-recovered GeneMark_model.106723_t, internal, 4657, 4710
-recovered GeneMark_model.106723_t, internal, 4738, 5013
-recovered GeneMark_model.106723_t, internal, 5040, 5183
-recovered GeneMark_model.106723_t, internal, 5247, 5286
-recovered GeneMark_model.106723_t, internal, 5530, 5642
-recovered GeneMark_model.106723_t, internal, 8049, 8090
-recovered GeneMark_model.106723_t, internal, 8449, 8484
Valid prediction for snap_scaffold_143-snap.3-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12083, rend_intergenic: 7078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 12759
-exon list size: 103


building trellis

1.0    
1.9    
2.9    
3.8    
4.8    
5.7    
6.7    
7.6    
8.6    
9.5    
10.5    
11.4    
12.4    
13.3    
14.3    
15.2    
16.2    
17.1    
18.1    
19.0    
20.0    
21.0    
21.9    
22.9    
23.8    
24.8    
25.7    
26.7    
27.6    
28.6    
29.5    
30.5    
31.4    
32.4    
33.3    
34.3    
35.2    
36.2    
37.1    
38.1    
39.0    
40.0    
41.0    
41.9    
42.9    
43.8    
44.8    
45.7    
46.7    
47.6    
48.6    
49.5    
50.5    
51.4    
52.4    
53.3    
54.3    
55.2    
56.2    
57.1    
58.1    
59.0    
60.0    
61.0    
61.9    
62.9    
63.8    
64.8    
65.7    
66.7    
67.6    
68.6    
69.5    
70.5    
71.4    
72.4    
73.3    
74.3    
75.2    
76.2    
77.1    
78.1    
79.0    
80.0    
81.0    
81.9    
82.9    
83.8    
84.8    
85.7    
86.7    
87.6    
88.6    
89.5    
90.5    
91.4    
92.4    
93.3    
94.3    
95.2    
96.2    
97.1    
98.1    
99.0    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 12083, rend_intergenic: 7078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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