-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_316

-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.107280_t
Couldn't classify 494, 578
Sorry, prediction GeneMark_model.107278_t fails validation.
(GTA)	 AG	494-578	GT	CAG
(ACA)	 AG	603-617	GT	GGG
(AGA)	 AG	677-859	GC	GAG
(TCA)	 AG	3194-3244	GT	GGG
(AGA)	 AG	3336-3389	GT	GAG
(GGC)	 AG	3427-3441	GT	CTG
(TCA)	 AG	3512-3674	CT	GAC
-recovered GeneMark_model.107278_t, terminal, 3512, 3674
-recovered GeneMark_model.107278_t, internal, 494, 578
-recovered GeneMark_model.107278_t, internal, 603, 617
-recovered GeneMark_model.107278_t, internal, 677, 859
-recovered GeneMark_model.107278_t, internal, 3194, 3244
-recovered GeneMark_model.107278_t, internal, 3336, 3389
-recovered GeneMark_model.107278_t, internal, 3427, 3441
Couldn't classify 494, 617
Sorry, prediction snap_scaffold_316-snap.1-T1 fails validation.
(GTA)	 AG	494-617	GT	GGG
(TCA)	 AG	3512-3674	CT	GAC
-recovered snap_scaffold_316-snap.1-T1, terminal, 3512, 3674
-recovered snap_scaffold_316-snap.1-T1, internal, 494, 617

-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 288, 408
Couldn't classify 7657, 7754
Sorry, prediction snap_scaffold_316-snap.2-T1 fails validation.
(GTC)	 AG	288-408	GT	TGG
(GGG)	 AG	801-898	GT	AGG
(GAA)	 AG	1276-1381	GT	AGG
(GTT)	 AG	2632-2674	GT	GAG
(TAT)	 AG	2899-2989	GT	GAG
(GCA)	 AG	3576-3581	GT	CAG
(AAC)	 AG	4472-4557	GT	CCG
(GAC)	 AG	4721-4793	GT	AAG
(GGA)	 AG	7657-7754	GT	AGG
-recovered snap_scaffold_316-snap.2-T1, terminal, 801, 898
-recovered snap_scaffold_316-snap.2-T1, internal, 288, 408
-recovered snap_scaffold_316-snap.2-T1, internal, 801, 898
-recovered snap_scaffold_316-snap.2-T1, internal, 1276, 1381
-recovered snap_scaffold_316-snap.2-T1, internal, 2632, 2674
-recovered snap_scaffold_316-snap.2-T1, internal, 2899, 2989
-recovered snap_scaffold_316-snap.2-T1, internal, 3576, 3581
-recovered snap_scaffold_316-snap.2-T1, internal, 4472, 4557
-recovered snap_scaffold_316-snap.2-T1, internal, 4721, 4793
-recovered snap_scaffold_316-snap.2-T1, internal, 7657, 7754
Couldn't classify 173, 408
Couldn't classify 1276, 1355
Sorry, prediction pasa_asmbl_40887.p1 fails validation.
(GTC)	 GT	173-408	GT	TGG
(GGG)	 AG	801-898	GT	AGG
(GAA)	 AG	1276-1355	CA	CCC
-recovered pasa_asmbl_40887.p1, terminal, 801, 898
-recovered pasa_asmbl_40887.p1, internal, 801, 898
Couldn't classify 288, 408
Couldn't classify 7657, 7754
Sorry, prediction Augustus_model.g41005.t1 fails validation.
(GTC)	 AG	288-408	GT	TGG
(GGG)	 AG	801-898	GT	AGG
(GAA)	 AG	1276-1381	GT	AGG
(GTT)	 AG	2632-2674	GT	GAG
(TAT)	 AG	2899-2989	GT	GAG
(GCA)	 AG	3576-3581	GT	CAG
(AAC)	 AG	4472-4584	GT	GGG
(CCA)	 AG	4995-5070	GT	AGG
(GGA)	 AG	7657-7754	GT	AGG
-recovered Augustus_model.g41005.t1, terminal, 801, 898
-recovered Augustus_model.g41005.t1, internal, 288, 408
-recovered Augustus_model.g41005.t1, internal, 801, 898
-recovered Augustus_model.g41005.t1, internal, 1276, 1381
-recovered Augustus_model.g41005.t1, internal, 2632, 2674
-recovered Augustus_model.g41005.t1, internal, 2899, 2989
-recovered Augustus_model.g41005.t1, internal, 3576, 3581
-recovered Augustus_model.g41005.t1, internal, 4472, 4584
-recovered Augustus_model.g41005.t1, internal, 4995, 5070
-recovered Augustus_model.g41005.t1, internal, 7657, 7754
Valid prediction for GeneMark_model.107279_t
Valid prediction for GeneMark_model.107281_t
add_exon() Sorry, GeneMark_model.107281_t 288-412-terminal-1 is invalid.
Couldn't classify 288, 408
Sorry, prediction GlimmerHMM_glimmerT_61685-T1 fails validation.
(GTC)	 AG	288-408	GT	TGG
(GGG)	 AG	801-898	GT	AGG
(GAA)	 AG	1276-1381	GT	AGG
(AAC)	 AG	4472-4557	GT	CCG
(GGA)	 AG	7657-7931	AG	AAA
-recovered GlimmerHMM_glimmerT_61685-T1, terminal, 801, 898
-recovered GlimmerHMM_glimmerT_61685-T1, terminal, 7657, 7931
-recovered GlimmerHMM_glimmerT_61685-T1, internal, 288, 408
-recovered GlimmerHMM_glimmerT_61685-T1, internal, 801, 898
-recovered GlimmerHMM_glimmerT_61685-T1, internal, 1276, 1381
-recovered GlimmerHMM_glimmerT_61685-T1, internal, 4472, 4557

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3674, rend_intergenic: 498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8251
-exon list size: 63


building trellis

1.5    
3.1    
4.6    
6.2    
7.7    
9.2    
10.8    
12.3    
13.8    
15.4    
16.9    
18.5    
20.0    
21.5    
23.1    
24.6    
26.2    
27.7    
29.2    
30.8    
32.3    
33.8    
35.4    
36.9    
38.5    
40.0    
41.5    
43.1    
44.6    
46.2    
47.7    
49.2    
50.8    
52.3    
53.8    
55.4    
56.9    
58.5    
60.0    
61.5    
63.1    
64.6    
66.2    
67.7    
69.2    
70.8    
72.3    
73.8    
75.4    
76.9    
78.5    
80.0    
81.5    
83.1    
84.6    
86.2    
87.7    
89.2    
90.8    
92.3    
93.8    
95.4    
96.9    
98.5    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 3674, rend_intergenic: 498  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