-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_490

-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 snap_scaffold_490-snap.2-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_490-snap.3-T1
Valid prediction for snap_scaffold_490-snap.1-T1
Valid prediction for snap_scaffold_490-snap.4-T1
Couldn't classify 855, 883
Sorry, prediction GeneMark_model.107778_t fails validation.
(ATC)	 AG	855-883	GT	GGG
(ACT)	 AG	1022-1090	GT	GGG
(ACT)	 AG	1124-1213	GC	CAG
(AGA)	 AG	1327-1396	GT	AAG
(AGA)	 AG	1416-1432	GT	GAG
(AGA)	 AG	1459-1503	GT	GGG
(GGA)	 AG	1556-1594	GT	ACG
(AAG)	 AG	1633-1689	GT	CTG
(TCC)	 AG	1744-1792	GT	TGG
(ACA)	 AG	1835-2043	GT	TGG
(GGA)	 AG	2136-2174	GT	AGG
(ACT)	 AG	2196-2315	GT	ATG
(ACT)	 AG	2342-2413	GT	ATG
(ACA)	 AG	2448-2525	GC	GAG
(ATC)	 AG	2549-2554	GT	GGG
(AGA)	 AG	2596-2628	GT	GAG
(GGA)	 AG	2669-2776	GT	AGG
(AGA)	 AG	2825-2830	GT	CTG
(AGA)	 AG	2888-3046	GT	GAG
(AGC)	 AG	3076-3099	GT	AGG
(AGG)	 AG	3125-3313	GT	GAG
(ACT)	 AG	3354-3666	GG	GAG
-recovered GeneMark_model.107778_t, terminal, 3354, 3666
-recovered GeneMark_model.107778_t, internal, 855, 883
-recovered GeneMark_model.107778_t, internal, 1022, 1090
-recovered GeneMark_model.107778_t, internal, 1124, 1213
-recovered GeneMark_model.107778_t, internal, 1327, 1396
-recovered GeneMark_model.107778_t, internal, 1416, 1432
-recovered GeneMark_model.107778_t, internal, 1459, 1503
-recovered GeneMark_model.107778_t, internal, 1556, 1594
-recovered GeneMark_model.107778_t, internal, 1633, 1689
-recovered GeneMark_model.107778_t, internal, 1744, 1792
-recovered GeneMark_model.107778_t, internal, 1835, 2043
-recovered GeneMark_model.107778_t, internal, 2136, 2174
-recovered GeneMark_model.107778_t, internal, 2196, 2315
-recovered GeneMark_model.107778_t, internal, 2342, 2413
-recovered GeneMark_model.107778_t, internal, 2448, 2525
-recovered GeneMark_model.107778_t, internal, 2549, 2554
-recovered GeneMark_model.107778_t, internal, 2596, 2628
-recovered GeneMark_model.107778_t, internal, 2669, 2776
-recovered GeneMark_model.107778_t, internal, 2825, 2830
-recovered GeneMark_model.107778_t, internal, 2888, 3046
-recovered GeneMark_model.107778_t, internal, 3076, 3099
-recovered GeneMark_model.107778_t, internal, 3125, 3313
Couldn't classify 764, 883
Sorry, prediction GlimmerHMM_glimmerT_61912-T1 fails validation.
(AAC)	 AG	764-883	GT	GGG
(GCA)	 AG	5554-5618	GT	AGG
(TCT)	 AG	5757-5931	CC	GAC
-recovered GlimmerHMM_glimmerT_61912-T1, terminal, 5757, 5931
-recovered GlimmerHMM_glimmerT_61912-T1, internal, 764, 883
-recovered GlimmerHMM_glimmerT_61912-T1, internal, 5554, 5618
Couldn't classify 5757, 5922
Sorry, prediction GeneMark_model.107776_t fails validation.
(ATG)	 GA	5611-5618	GT	AGG
(TCT)	 AG	5757-5922	GT	GAG
-recovered GeneMark_model.107776_t, initial, 5611, 5618
-recovered GeneMark_model.107776_t, internal, 5757, 5922
Valid prediction for GeneMark_model.107777_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5723, rend_intergenic: 2476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6530
-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 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 5723, rend_intergenic: 2476  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