-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_476

-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 GeneMark_model.107736_t
Couldn't classify 123, 233
Couldn't classify 4777, 4888
Sorry, prediction snap_scaffold_476-snap.2-T1 fails validation.
(GAA)	 AG	123-233	GT	CGG
(GGC)	 AG	255-387	GT	GAG
(GCG)	 AG	2027-2100	GT	CCG
(TCG)	 AG	2690-2834	GT	CTG
(ATT)	 AG	2995-3146	GT	AAG
(TAC)	 AG	3596-3799	GT	GGG
(CCT)	 AG	4777-4888	GT	TGG
-recovered snap_scaffold_476-snap.2-T1, internal, 123, 233
-recovered snap_scaffold_476-snap.2-T1, internal, 255, 387
-recovered snap_scaffold_476-snap.2-T1, internal, 2027, 2100
-recovered snap_scaffold_476-snap.2-T1, internal, 2690, 2834
-recovered snap_scaffold_476-snap.2-T1, internal, 2995, 3146
-recovered snap_scaffold_476-snap.2-T1, internal, 3596, 3799
-recovered snap_scaffold_476-snap.2-T1, internal, 4777, 4888

-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 470, 519
Sorry, prediction GeneMark_model.107737_t fails validation.
(TCT)	 AG	470-519	GT	AGG
(GGG)	 AG	652-759	GT	GAG
(AGA)	 AG	782-829	GT	GAG
(AGG)	 AG	857-865	GT	GAG
(AGG)	 AG	892-903	GT	AGG
(AGG)	 AG	929-944	AG	GAA
-recovered GeneMark_model.107737_t, terminal, 929, 944
-recovered GeneMark_model.107737_t, internal, 470, 519
-recovered GeneMark_model.107737_t, internal, 652, 759
-recovered GeneMark_model.107737_t, internal, 782, 829
-recovered GeneMark_model.107737_t, internal, 857, 865
-recovered GeneMark_model.107737_t, internal, 892, 903
Couldn't classify 3883, 4016
Couldn't classify 5590, 5729
Sorry, prediction pasa_asmbl_43714.p1 fails validation.
(AAC)	 AG	3883-4016	GT	AGG
(ACG)	 AG	4529-4659	GT	CGG
(GTT)	 AG	5590-5729	CG	AAC
-recovered pasa_asmbl_43714.p1, internal, 3883, 4016
-recovered pasa_asmbl_43714.p1, internal, 4529, 4659
Couldn't classify 470, 519
Couldn't classify 6348, 6635
Sorry, prediction snap_scaffold_476-snap.1-T1 fails validation.
(TCT)	 AG	470-519	GT	AGG
(TAT)	 AG	1771-1967	GT	AGG
(ACG)	 AG	2323-2419	GT	CTG
(GTC)	 AG	2508-2623	GT	AGG
(TTG)	 AG	2873-3014	GT	ATG
(GTG)	 AG	3437-3653	GT	AGG
(AAC)	 AG	3883-4016	GT	AGG
(ACG)	 AG	4529-4659	GT	CGG
(GTT)	 AG	5590-5698	GT	GAG
(CAC)	 AG	6015-6186	GT	CGG
(AGC)	 AG	6348-6635	GT	AGG
add_exon() Sorry, snap_scaffold_476-snap.1-T1 5590-5698-terminal-3 is invalid.
-recovered snap_scaffold_476-snap.1-T1, terminal, 5590, 5698
-recovered snap_scaffold_476-snap.1-T1, internal, 470, 519
-recovered snap_scaffold_476-snap.1-T1, internal, 1771, 1967
-recovered snap_scaffold_476-snap.1-T1, internal, 2323, 2419
-recovered snap_scaffold_476-snap.1-T1, internal, 2508, 2623
-recovered snap_scaffold_476-snap.1-T1, internal, 2873, 3014
-recovered snap_scaffold_476-snap.1-T1, internal, 3437, 3653
-recovered snap_scaffold_476-snap.1-T1, internal, 3883, 4016
-recovered snap_scaffold_476-snap.1-T1, internal, 4529, 4659
-recovered snap_scaffold_476-snap.1-T1, internal, 5590, 5698
-recovered snap_scaffold_476-snap.1-T1, internal, 6015, 6186
-recovered snap_scaffold_476-snap.1-T1, internal, 6348, 6635
Couldn't classify 470, 519
Sorry, prediction GlimmerHMM_glimmerT_61896-T1 fails validation.
(TCT)	 AG	470-519	GT	AGG
(TAT)	 AG	1771-1967	GT	AGG
(ACG)	 AG	2323-2419	GT	CTG
(GTC)	 AG	2508-2631	GT	GAG
-recovered GlimmerHMM_glimmerT_61896-T1, terminal, 2508, 2631
-recovered GlimmerHMM_glimmerT_61896-T1, internal, 470, 519
-recovered GlimmerHMM_glimmerT_61896-T1, internal, 1771, 1967
-recovered GlimmerHMM_glimmerT_61896-T1, internal, 2323, 2419
-recovered GlimmerHMM_glimmerT_61896-T1, internal, 2508, 2631
Couldn't classify 6348, 6625
Sorry, prediction GeneMark_model.107735_t fails validation.
(ATG)	 CC	1982-1993	GT	TAG
(GAC)	 AG	2328-2419	GT	CTG
(AAA)	 AG	2589-2623	GT	AGG
(TTG)	 AG	2873-3057	GT	TTG
(GTG)	 AG	3489-3653	GT	AGG
(AAC)	 AG	3883-4016	GT	AGG
(GGG)	 AG	4744-4786	GT	AAG
(GTT)	 AG	5590-5666	GT	ATG
(GGG)	 AG	5769-5783	GT	AGG
(GGA)	 AG	5806-5838	GT	TGG
(CAC)	 AG	6015-6186	GT	CGG
(AGC)	 AG	6348-6625	GT	CTG
-recovered GeneMark_model.107735_t, initial, 1982, 1993
-recovered GeneMark_model.107735_t, internal, 2328, 2419
-recovered GeneMark_model.107735_t, internal, 2589, 2623
-recovered GeneMark_model.107735_t, internal, 2873, 3057
-recovered GeneMark_model.107735_t, internal, 3489, 3653
-recovered GeneMark_model.107735_t, internal, 3883, 4016
-recovered GeneMark_model.107735_t, internal, 4744, 4786
-recovered GeneMark_model.107735_t, internal, 5590, 5666
-recovered GeneMark_model.107735_t, internal, 5769, 5783
-recovered GeneMark_model.107735_t, internal, 5806, 5838
-recovered GeneMark_model.107735_t, internal, 6015, 6186
-recovered GeneMark_model.107735_t, internal, 6348, 6625
Valid prediction for GlimmerHMM_glimmerT_61895-T1
Couldn't classify 470, 519
Couldn't classify 6348, 6635
Sorry, prediction Augustus_model.g41144.t1 fails validation.
(TCT)	 AG	470-519	GT	AGG
(TAT)	 AG	1771-1967	GT	AGG
(ACG)	 AG	2323-2419	GT	CTG
(GTC)	 AG	2508-2623	GT	AGG
(TTG)	 AG	2873-3014	GT	ATG
(AGG)	 AG	3541-3679	GT	ATG
(AAC)	 AG	3883-4016	GT	AGG
(ACG)	 AG	4529-4659	GT	CGG
(GTT)	 AG	5590-5646	GT	CGG
(CAA)	 AG	5727-5748	GT	AGG
(CAC)	 AG	6015-6186	GT	CGG
(AGC)	 AG	6348-6635	GT	AGG
-recovered Augustus_model.g41144.t1, internal, 470, 519
-recovered Augustus_model.g41144.t1, internal, 1771, 1967
-recovered Augustus_model.g41144.t1, internal, 2323, 2419
-recovered Augustus_model.g41144.t1, internal, 2508, 2623
-recovered Augustus_model.g41144.t1, internal, 2873, 3014
-recovered Augustus_model.g41144.t1, internal, 3541, 3679
-recovered Augustus_model.g41144.t1, internal, 3883, 4016
-recovered Augustus_model.g41144.t1, internal, 4529, 4659
-recovered Augustus_model.g41144.t1, internal, 5590, 5646
-recovered Augustus_model.g41144.t1, internal, 5727, 5748
-recovered Augustus_model.g41144.t1, internal, 6015, 6186
-recovered Augustus_model.g41144.t1, internal, 6348, 6635

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6186, rend_intergenic: 123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6655
-exon list size: 75


building trellis

1.3    
2.6    
3.9    
5.2    
6.5    
7.8    
9.1    
10.4    
11.7    
13.0    
14.3    
15.6    
16.9    
18.2    
19.5    
20.8    
22.1    
23.4    
24.7    
26.0    
27.3    
28.6    
29.9    
31.2    
32.5    
33.8    
35.1    
36.4    
37.7    
39.0    
40.3    
41.6    
42.9    
44.2    
45.5    
46.8    
48.1    
49.4    
50.6    
51.9    
53.2    
54.5    
55.8    
57.1    
58.4    
59.7    
61.0    
62.3    
63.6    
64.9    
66.2    
67.5    
68.8    
70.1    
71.4    
72.7    
74.0    
75.3    
76.6    
77.9    
79.2    
80.5    
81.8    
83.1    
84.4    
85.7    
87.0    
88.3    
89.6    
90.9    
92.2    
93.5    
94.8    
96.1    
97.4    
98.7    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 6186, rend_intergenic: 123  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