-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_254

-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 36, 41
Sorry, prediction GeneMark_model.107088_t fails validation.
(AAT)	 AG	36-41	GT	AGG
(GTT)	 AG	64-135	GT	TTG
(TGA)	 AG	1361-1472	GT	GAG
(GAG)	 AG	1764-1798	GT	GGG
(GGA)	 AG	1826-1849	GT	AGG
(GGA)	 AG	1878-1901	GT	AGG
(GGA)	 AG	1930-2124	GT	TTG
(AGA)	 AG	2150-2305	GT	AGG
(ACA)	 AG	2332-2382	GT	GTG
(AGA)	 AG	2410-2418	GT	GTG
(AGA)	 AG	2446-2454	GT	GTG
(AGA)	 AG	2481-2489	GT	GAG
(AGA)	 AG	2517-2576	GT	GTG
(ACA)	 AG	2600-2629	GT	GTG
(ACA)	 AG	2653-2682	GT	GTG
(AGG)	 AG	2725-2739	GT	AGG
(AGA)	 AG	3078-3086	GC	GAG
(AGA)	 AG	3116-3338	GG	GAG
-recovered GeneMark_model.107088_t, terminal, 3116, 3338
-recovered GeneMark_model.107088_t, internal, 36, 41
-recovered GeneMark_model.107088_t, internal, 64, 135
-recovered GeneMark_model.107088_t, internal, 1361, 1472
-recovered GeneMark_model.107088_t, internal, 1764, 1798
-recovered GeneMark_model.107088_t, internal, 1826, 1849
-recovered GeneMark_model.107088_t, internal, 1878, 1901
-recovered GeneMark_model.107088_t, internal, 1930, 2124
-recovered GeneMark_model.107088_t, internal, 2150, 2305
-recovered GeneMark_model.107088_t, internal, 2332, 2382
-recovered GeneMark_model.107088_t, internal, 2410, 2418
-recovered GeneMark_model.107088_t, internal, 2446, 2454
-recovered GeneMark_model.107088_t, internal, 2481, 2489
-recovered GeneMark_model.107088_t, internal, 2517, 2576
-recovered GeneMark_model.107088_t, internal, 2600, 2629
-recovered GeneMark_model.107088_t, internal, 2653, 2682
-recovered GeneMark_model.107088_t, internal, 2725, 2739
-recovered GeneMark_model.107088_t, internal, 3078, 3086
Valid prediction for snap_scaffold_254-snap.2-T1
Valid prediction for GeneMark_model.107091_t

-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.107090_t
Valid prediction for snap_scaffold_254-snap.1-T1
Valid prediction for GeneMark_model.107089_t
Couldn't classify 15, 846
Sorry, prediction pasa_asmbl_34625.p1 fails validation.
(AGA)	 CA	15-846	GT	AGG
(TGG)	 AG	1618-1787	AG	AGA
-recovered pasa_asmbl_34625.p1, terminal, 1618, 1787
Couldn't classify 102, 846
Sorry, prediction GlimmerHMM_glimmerT_61585-T1 fails validation.
(CTG)	 AG	102-846	GT	AGG
(TGG)	 AG	1618-1787	AG	AGA
-recovered GlimmerHMM_glimmerT_61585-T1, terminal, 1618, 1787
-recovered GlimmerHMM_glimmerT_61585-T1, internal, 102, 846
Valid prediction for CodingQuarry_transcript_38757-T1
Couldn't classify 17, 175
Sorry, prediction GeneMark_model.107092_t fails validation.
(AGT)	 AG	17-175	GT	CCG
(GAA)	 AG	222-338	GT	AAG
(TGC)	 AG	380-719	GT	TTG
(ACC)	 AG	781-807	AC	AAA
-recovered GeneMark_model.107092_t, terminal, 781, 807
-recovered GeneMark_model.107092_t, internal, 17, 175
-recovered GeneMark_model.107092_t, internal, 222, 338
-recovered GeneMark_model.107092_t, internal, 380, 719
Couldn't classify 102, 750
Sorry, prediction snap_scaffold_254-snap.3-T1 fails validation.
(CTG)	 AG	102-750	GT	AAG
(TGG)	 AG	1618-1787	AG	AGA
-recovered snap_scaffold_254-snap.3-T1, terminal, 1618, 1787
-recovered snap_scaffold_254-snap.3-T1, internal, 102, 750

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6827, rend_intergenic: 5642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8902, rend_intergenic: 7213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8999
-exon list size: 65


building trellis

1.5    
3.0    
4.5    
6.0    
7.5    
9.0    
10.4    
11.9    
13.4    
14.9    
16.4    
17.9    
19.4    
20.9    
22.4    
23.9    
25.4    
26.9    
28.4    
29.9    
31.3    
32.8    
34.3    
35.8    
37.3    
38.8    
40.3    
41.8    
43.3    
44.8    
46.3    
47.8    
49.3    
50.7    
52.2    
53.7    
55.2    
56.7    
58.2    
59.7    
61.2    
62.7    
64.2    
65.7    
67.2    
68.7    
70.1    
71.6    
73.1    
74.6    
76.1    
77.6    
79.1    
80.6    
82.1    
83.6    
85.1    
86.6    
88.1    
89.6    
91.0    
92.5    
94.0    
95.5    
97.0    
98.5    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 6827, rend_intergenic: 5642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8902, rend_intergenic: 7213  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