-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_310

-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 6962, 7057
Sorry, prediction GlimmerHMM_glimmerT_61674-T1 fails validation.
(ATG)	 AG	483-545	GT	AGG
(GGG)	 AG	6056-6256	GT	GAG
(GGG)	 AG	6962-7057	GT	GGG
-recovered GlimmerHMM_glimmerT_61674-T1, initial, 483, 545
-recovered GlimmerHMM_glimmerT_61674-T1, internal, 483, 545
-recovered GlimmerHMM_glimmerT_61674-T1, internal, 6056, 6256
-recovered GlimmerHMM_glimmerT_61674-T1, internal, 6962, 7057
Couldn't classify 224, 428
Sorry, prediction GeneMark_model.107262_t fails validation.
(GGC)	 AG	224-428	GT	AAG
(AGG)	 AG	451-474	GT	GAG
(GGG)	 AG	518-545	GT	AGG
(CAG)	 AG	711-749	CC	GAC
-recovered GeneMark_model.107262_t, terminal, 711, 749
-recovered GeneMark_model.107262_t, internal, 224, 428
-recovered GeneMark_model.107262_t, internal, 451, 474
-recovered GeneMark_model.107262_t, internal, 518, 545
Valid prediction for snap_scaffold_310-snap.3-T1
Couldn't classify 6962, 7057
Sorry, prediction snap_scaffold_310-snap.4-T1 fails validation.
(ATG)	 TG	3720-3742	GT	GAG
(ATG)	 AG	6043-6256	GT	GAG
(GGG)	 AG	6962-7057	GT	GGG
-recovered snap_scaffold_310-snap.4-T1, initial, 3720, 3742
add_exon() Sorry, snap_scaffold_310-snap.4-T1 6043-6256-initial-1 is invalid.
-recovered snap_scaffold_310-snap.4-T1, initial, 6043, 6256
-recovered snap_scaffold_310-snap.4-T1, internal, 6043, 6256
-recovered snap_scaffold_310-snap.4-T1, internal, 6962, 7057
Valid prediction for GeneMark_model.107263_t
Couldn't classify 224, 409
Sorry, prediction snap_scaffold_310-snap.2-T1 fails validation.
(GGC)	 AG	224-409	GT	AGG
(GGG)	 AG	436-545	GT	AGG
(CGA)	 AG	1549-1608	TT	AAT
-recovered snap_scaffold_310-snap.2-T1, terminal, 1549, 1608
-recovered snap_scaffold_310-snap.2-T1, internal, 224, 409
-recovered snap_scaffold_310-snap.2-T1, internal, 436, 545
Couldn't classify 8116, 8167
Sorry, prediction GeneMark_model.107264_t fails validation.
(ATG)	 GA	3717-3742	GT	GAG
(GAT)	 AG	3764-3778	GT	AAG
(CTT)	 AG	6064-6216	GT	GCG
(GGG)	 AG	6962-7057	GT	GGG
(ACA)	 AG	7087-7118	GT	GAG
(ACA)	 AG	8116-8167	GT	GAG
-recovered GeneMark_model.107264_t, initial, 3717, 3742
-recovered GeneMark_model.107264_t, internal, 3764, 3778
-recovered GeneMark_model.107264_t, internal, 6064, 6216
-recovered GeneMark_model.107264_t, internal, 6962, 7057
-recovered GeneMark_model.107264_t, internal, 7087, 7118
-recovered GeneMark_model.107264_t, internal, 8116, 8167

-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 2038, 2196
Couldn't classify 8083, 8137
Sorry, prediction snap_scaffold_310-snap.1-T1 fails validation.
(ACG)	 AG	2038-2196	GT	AGG
(GGT)	 AG	3600-3767	GT	TGG
(ACA)	 AG	7560-7625	GT	TAG
(CAT)	 AG	8008-8015	GT	GGG
(GAC)	 AG	8083-8137	GT	GGG
-recovered snap_scaffold_310-snap.1-T1, internal, 2038, 2196
-recovered snap_scaffold_310-snap.1-T1, internal, 3600, 3767
-recovered snap_scaffold_310-snap.1-T1, internal, 7560, 7625
-recovered snap_scaffold_310-snap.1-T1, internal, 8008, 8015
-recovered snap_scaffold_310-snap.1-T1, internal, 8083, 8137

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6262, rend_intergenic: 224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8299
-exon list size: 43


building trellis

2.2    
4.4    
6.7    
8.9    
11.1    
13.3    
15.6    
17.8    
20.0    
22.2    
24.4    
26.7    
28.9    
31.1    
33.3    
35.6    
37.8    
40.0    
42.2    
44.4    
46.7    
48.9    
51.1    
53.3    
55.6    
57.8    
60.0    
62.2    
64.4    
66.7    
68.9    
71.1    
73.3    
75.6    
77.8    
80.0    
82.2    
84.4    
86.7    
88.9    
91.1    
93.3    
95.6    
97.8    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 6262, rend_intergenic: 224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support