-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_847

-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.108480_t
Couldn't classify 44, 241
Couldn't classify 4086, 4159
Sorry, prediction snap_scaffold_847-snap.1-T1 fails validation.
(CTC)	 AG	44-241	GT	TGG
(CCA)	 AG	686-729	GT	CGG
(GGA)	 AG	2203-2373	GT	GGG
(TGG)	 AG	2382-2491	GT	AGG
(TTC)	 AG	2725-2898	GT	GAG
(ACC)	 AG	3288-3370	GT	GGG
(GGA)	 AG	4086-4159	GT	AGG
add_exon() Sorry, snap_scaffold_847-snap.1-T1 2382-2491-terminal-2 is invalid.
-recovered snap_scaffold_847-snap.1-T1, terminal, 2382, 2491
-recovered snap_scaffold_847-snap.1-T1, internal, 44, 241
-recovered snap_scaffold_847-snap.1-T1, internal, 686, 729
-recovered snap_scaffold_847-snap.1-T1, internal, 2203, 2373
-recovered snap_scaffold_847-snap.1-T1, internal, 2382, 2491
-recovered snap_scaffold_847-snap.1-T1, internal, 2725, 2898
-recovered snap_scaffold_847-snap.1-T1, internal, 3288, 3370
-recovered snap_scaffold_847-snap.1-T1, internal, 4086, 4159
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 2436, 2491
Couldn't classify 4086, 4159
Sorry, prediction pasa_asmbl_53688.p1 fails validation.
(GCA)	 AG	2436-2491	GT	AGG
(TTC)	 AG	2725-2898	GT	GAG
(ACC)	 AG	3288-3370	GT	GGG
(GGA)	 AG	4086-4159	GT	AGG
-recovered pasa_asmbl_53688.p1, terminal, 2436, 2491
-recovered pasa_asmbl_53688.p1, internal, 2436, 2491
-recovered pasa_asmbl_53688.p1, internal, 2725, 2898
-recovered pasa_asmbl_53688.p1, internal, 3288, 3370
-recovered pasa_asmbl_53688.p1, internal, 4086, 4159
Valid prediction for Augustus_model.g41402.t1
Valid prediction for GlimmerHMM_glimmerT_62289-T1
Valid prediction for GlimmerHMM_glimmerT_62288-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: -)Couldn't classify 179, 226
Sorry, prediction GeneMark_model.108481_t fails validation.
(AGA)	 AG	179-226	GC	AGG
(AAA)	 AG	253-273	GT	GAG
(AGA)	 AG	297-438	AT	GAA
-recovered GeneMark_model.108481_t, terminal, 297, 438
-recovered GeneMark_model.108481_t, internal, 179, 226
-recovered GeneMark_model.108481_t, internal, 253, 273
Couldn't classify 1510, 1616
Sorry, prediction snap_scaffold_847-snap.2-T1 fails validation.
(AAC)	 AG	1510-1616	GT	CTG
(GGG)	 AG	2009-2178	GT	GGG
(ATT)	 AG	3489-3579	AC	AGA
-recovered snap_scaffold_847-snap.2-T1, terminal, 3489, 3579
-recovered snap_scaffold_847-snap.2-T1, internal, 1510, 1616
-recovered snap_scaffold_847-snap.2-T1, internal, 2009, 2178
Couldn't classify 2979, 2984
Sorry, prediction GeneMark_model.108479_t fails validation.
(ATG)	 GG	2052-2146	GT	GCG
(AAG)	 AG	2167-2178	GT	GGG
(GGG)	 AG	2203-2340	GT	AGG
(AAA)	 AG	2375-2386	GT	CTG
(AAA)	 AG	2407-2508	GT	GGG
(AGG)	 AG	2531-2548	GT	AGG
(AGA)	 AG	2571-2643	GT	AGG
(AGG)	 AG	2979-2984	GT	AGG
-recovered GeneMark_model.108479_t, initial, 2052, 2146
-recovered GeneMark_model.108479_t, internal, 2167, 2178
-recovered GeneMark_model.108479_t, internal, 2203, 2340
-recovered GeneMark_model.108479_t, internal, 2375, 2386
-recovered GeneMark_model.108479_t, internal, 2407, 2508
-recovered GeneMark_model.108479_t, internal, 2531, 2548
-recovered GeneMark_model.108479_t, internal, 2571, 2643
-recovered GeneMark_model.108479_t, internal, 2979, 2984

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4159, rend_intergenic: 657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 4235
-exon list size: 58


building trellis

1.7    
3.3    
5.0    
6.7    
8.3    
10.0    
11.7    
13.3    
15.0    
16.7    
18.3    
20.0    
21.7    
23.3    
25.0    
26.7    
28.3    
30.0    
31.7    
33.3    
35.0    
36.7    
38.3    
40.0    
41.7    
43.3    
45.0    
46.7    
48.3    
50.0    
51.7    
53.3    
55.0    
56.7    
58.3    
60.0    
61.7    
63.3    
65.0    
66.7    
68.3    
70.0    
71.7    
73.3    
75.0    
76.7    
78.3    
80.0    
81.7    
83.3    
85.0    
86.7    
88.3    
90.0    
91.7    
93.3    
95.0    
96.7    
98.3    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 4159, rend_intergenic: 657  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