-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_618

-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 4741, 5118
Sorry, prediction GeneMark_model.108055_t fails validation.
(ATG)	 GA	4176-4192	GT	GAG
(ACC)	 AG	4262-4612	GT	CAG
(ATG)	 AG	4741-5118	GT	CTG
-recovered GeneMark_model.108055_t, initial, 4176, 4192
-recovered GeneMark_model.108055_t, initial, 4741, 5118
-recovered GeneMark_model.108055_t, internal, 4262, 4612
-recovered GeneMark_model.108055_t, internal, 4741, 5118
Valid prediction for GlimmerHMM_glimmerT_62055-T1
Valid prediction for GeneMark_model.108053_t
Couldn't classify 53, 58
Sorry, prediction GeneMark_model.108051_t fails validation.
(GAG)	 AG	53-58	GT	TTG
(AGG)	 AG	91-108	GT	TTG
(AGG)	 AG	131-148	GT	GAG
(GAG)	 AG	173-178	GT	TCG
(AGG)	 AG	211-228	GT	GAG
(GAG)	 AG	253-258	GT	TCG
(GAG)	 AG	280-285	GT	TTG
(GCT)	 AG	326-416	GG	GAG
add_exon() Sorry, GeneMark_model.108051_t 131-148-terminal-1 is invalid.
-recovered GeneMark_model.108051_t, terminal, 131, 148
add_exon() Sorry, GeneMark_model.108051_t 211-228-terminal-1 is invalid.
-recovered GeneMark_model.108051_t, terminal, 211, 228
-recovered GeneMark_model.108051_t, terminal, 326, 416
-recovered GeneMark_model.108051_t, internal, 53, 58
-recovered GeneMark_model.108051_t, internal, 91, 108
-recovered GeneMark_model.108051_t, internal, 131, 148
-recovered GeneMark_model.108051_t, internal, 173, 178
-recovered GeneMark_model.108051_t, internal, 211, 228
-recovered GeneMark_model.108051_t, internal, 253, 258
-recovered GeneMark_model.108051_t, internal, 280, 285
Valid prediction for snap_scaffold_618-snap.1-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 GeneMark_model.108052_t
Couldn't classify 1023, 1103
Sorry, prediction Augustus_model.g41247.t1 fails validation.
(GGC)	 AG	1023-1103	GT	CGG
(GGT)	 AG	1555-1664	GT	AGG
(GGC)	 AG	2065-2146	GT	AGG
(GTG)	 AG	3483-3599	GT	AGG
(GCG)	 AG	3894-4121	GG	GAG
-recovered Augustus_model.g41247.t1, terminal, 3894, 4121
-recovered Augustus_model.g41247.t1, internal, 1023, 1103
-recovered Augustus_model.g41247.t1, internal, 1555, 1664
-recovered Augustus_model.g41247.t1, internal, 2065, 2146
-recovered Augustus_model.g41247.t1, internal, 3483, 3599
Valid prediction for GeneMark_model.108054_t
Couldn't classify 752, 1103
Couldn't classify 3894, 4117
Sorry, prediction snap_scaffold_618-snap.2-T1 fails validation.
(TAC)	 AG	752-1103	GT	CGG
(GGT)	 AG	1555-1664	GT	AGG
(GGC)	 AG	2065-2146	GT	AGG
(TTC)	 AG	3141-3179	GT	AGG
(GCG)	 AG	3894-4117	GT	AGG
-recovered snap_scaffold_618-snap.2-T1, internal, 752, 1103
-recovered snap_scaffold_618-snap.2-T1, internal, 1555, 1664
-recovered snap_scaffold_618-snap.2-T1, internal, 2065, 2146
-recovered snap_scaffold_618-snap.2-T1, internal, 3141, 3179
-recovered snap_scaffold_618-snap.2-T1, internal, 3894, 4117
Valid prediction for GlimmerHMM_glimmerT_62054-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4597, rend_intergenic: 1250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5366
-exon list size: 66


building trellis

1.5    
2.9    
4.4    
5.9    
7.4    
8.8    
10.3    
11.8    
13.2    
14.7    
16.2    
17.6    
19.1    
20.6    
22.1    
23.5    
25.0    
26.5    
27.9    
29.4    
30.9    
32.4    
33.8    
35.3    
36.8    
38.2    
39.7    
41.2    
42.6    
44.1    
45.6    
47.1    
48.5    
50.0    
51.5    
52.9    
54.4    
55.9    
57.4    
58.8    
60.3    
61.8    
63.2    
64.7    
66.2    
67.6    
69.1    
70.6    
72.1    
73.5    
75.0    
76.5    
77.9    
79.4    
80.9    
82.4    
83.8    
85.3    
86.8    
88.2    
89.7    
91.2    
92.6    
94.1    
95.6    
97.1    
98.5    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 4597, rend_intergenic: 1250  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