-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_406

-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 6706, 6791
Sorry, prediction GlimmerHMM_glimmerT_61807-T1 fails validation.
(ATG)	 CC	1745-1971	GT	AGG
(GGC)	 AG	5360-5506	GT	AGG
(TTG)	 AG	5967-6064	GT	AGG
(AGG)	 AG	6706-6791	GT	GGG
-recovered GlimmerHMM_glimmerT_61807-T1, initial, 1745, 1971
-recovered GlimmerHMM_glimmerT_61807-T1, internal, 5360, 5506
-recovered GlimmerHMM_glimmerT_61807-T1, internal, 5967, 6064
-recovered GlimmerHMM_glimmerT_61807-T1, internal, 6706, 6791
Valid prediction for GeneMark_model.107550_t
Valid prediction for Augustus_model.g41079.t1
Valid prediction for GeneMark_model.107548_t
Couldn't classify 1404, 1549
Couldn't classify 6706, 6850
Sorry, prediction snap_scaffold_406-snap.1-T1 fails validation.
(CTC)	 AG	1404-1549	GT	AGG
(GGG)	 AG	1717-1971	GT	AGG
(AAC)	 AG	3257-3420	GT	GGG
(GGC)	 AG	3692-3857	GT	GGG
(GGC)	 AG	5158-5185	GT	AGG
(GAC)	 AG	5370-5506	GT	AGG
(TTG)	 AG	5967-6064	GT	AGG
(AGG)	 AG	6706-6850	GT	CGG
-recovered snap_scaffold_406-snap.1-T1, terminal, 1404, 1549
-recovered snap_scaffold_406-snap.1-T1, internal, 1404, 1549
-recovered snap_scaffold_406-snap.1-T1, internal, 1717, 1971
-recovered snap_scaffold_406-snap.1-T1, internal, 3257, 3420
-recovered snap_scaffold_406-snap.1-T1, internal, 3692, 3857
-recovered snap_scaffold_406-snap.1-T1, internal, 5158, 5185
-recovered snap_scaffold_406-snap.1-T1, internal, 5370, 5506
-recovered snap_scaffold_406-snap.1-T1, internal, 5967, 6064
-recovered snap_scaffold_406-snap.1-T1, internal, 6706, 6850

-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_406-snap.2-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.107549_t
Valid prediction for GeneMark_model.107551_t
Couldn't classify 33, 95
Sorry, prediction GeneMark_model.107552_t fails validation.
(GGA)	 AG	33-95	GT	GCG
(GTC)	 AG	310-408	GT	GGG
(GGA)	 AG	509-595	GT	GAG
(AGA)	 AG	629-727	GC	AGG
(GCA)	 AG	756-903	AG	AGA
add_exon() Sorry, GeneMark_model.107552_t 629-727-terminal-1 is invalid.
-recovered GeneMark_model.107552_t, terminal, 629, 727
-recovered GeneMark_model.107552_t, terminal, 756, 903
-recovered GeneMark_model.107552_t, internal, 33, 95
-recovered GeneMark_model.107552_t, internal, 310, 408
-recovered GeneMark_model.107552_t, internal, 509, 595
-recovered GeneMark_model.107552_t, internal, 629, 727

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6850, rend_intergenic: 2859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 7232
-exon list size: 61


building trellis

1.6    
3.2    
4.8    
6.3    
7.9    
9.5    
11.1    
12.7    
14.3    
15.9    
17.5    
19.0    
20.6    
22.2    
23.8    
25.4    
27.0    
28.6    
30.2    
31.7    
33.3    
34.9    
36.5    
38.1    
39.7    
41.3    
42.9    
44.4    
46.0    
47.6    
49.2    
50.8    
52.4    
54.0    
55.6    
57.1    
58.7    
60.3    
61.9    
63.5    
65.1    
66.7    
68.3    
69.8    
71.4    
73.0    
74.6    
76.2    
77.8    
79.4    
81.0    
82.5    
84.1    
85.7    
87.3    
88.9    
90.5    
92.1    
93.7    
95.2    
96.8    
98.4    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 6850, rend_intergenic: 2859  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