-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_402

-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.107537_t
Couldn't classify 239, 376
Couldn't classify 6569, 6651
Sorry, prediction snap_scaffold_402-snap.2-T1 fails validation.
(GGA)	 AG	239-376	GT	GGG
(GAT)	 AG	573-845	GT	GGG
(GAG)	 AG	4055-4135	GT	GGG
(CTC)	 AG	5776-5833	GT	CGG
(TTC)	 AG	6569-6651	GT	AGG
-recovered snap_scaffold_402-snap.2-T1, internal, 239, 376
-recovered snap_scaffold_402-snap.2-T1, internal, 573, 845
-recovered snap_scaffold_402-snap.2-T1, internal, 4055, 4135
-recovered snap_scaffold_402-snap.2-T1, internal, 5776, 5833
-recovered snap_scaffold_402-snap.2-T1, internal, 6569, 6651
Couldn't classify 6564, 6725
Sorry, prediction GlimmerHMM_glimmerT_61802-T1 fails validation.
(ATG)	 AT	5751-5833	GT	CGG
(TCC)	 AG	6564-6725	GT	TCG
-recovered GlimmerHMM_glimmerT_61802-T1, initial, 5751, 5833
-recovered GlimmerHMM_glimmerT_61802-T1, internal, 6564, 6725

-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 GlimmerHMM_glimmerT_61801-T1
Couldn't classify 6955, 7069
Sorry, prediction snap_scaffold_402-snap.1-T1 fails validation.
(ATG)	 TA	1411-1479	GT	CGG
(ATA)	 AG	3071-3123	GT	ATG
(CCC)	 AG	3146-3698	GT	CGG
(TTT)	 AG	6491-6739	GT	AGG
(GTC)	 AG	6955-7069	GT	CTG
-recovered snap_scaffold_402-snap.1-T1, initial, 1411, 1479
-recovered snap_scaffold_402-snap.1-T1, internal, 3071, 3123
-recovered snap_scaffold_402-snap.1-T1, internal, 3146, 3698
-recovered snap_scaffold_402-snap.1-T1, internal, 6491, 6739
-recovered snap_scaffold_402-snap.1-T1, internal, 6955, 7069
Valid prediction for Augustus_model.g41075.t1
Valid prediction for CodingQuarry_transcript_49321-T1
Couldn't classify 529, 562
Sorry, prediction GeneMark_model.107540_t fails validation.
(GCA)	 AG	529-562	GT	TGG
(TCG)	 AG	637-665	GT	AAG
(AAA)	 AG	798-978	GA	AGG
-recovered GeneMark_model.107540_t, terminal, 798, 978
-recovered GeneMark_model.107540_t, internal, 529, 562
-recovered GeneMark_model.107540_t, internal, 637, 665
Valid prediction for GeneMark_model.107539_t
Valid prediction for GeneMark_model.107538_t
Valid prediction for Augustus_model.g41076.t1
Valid prediction for GeneMark_model.107536_t
Couldn't classify 3377, 3701
Sorry, prediction pasa_asmbl_43649.p1 fails validation.
(ATG)	 CG	3078-3097	GT	CAG
(GGG)	 AG	3377-3701	GA	TGG
-recovered pasa_asmbl_43649.p1, initial, 3078, 3097
Couldn't classify 6491, 6739
Sorry, prediction pasa_asmbl_43648.p1 fails validation.
(TTT)	 AG	6491-6739	GT	AGG
(GTC)	 AG	6955-7128	CA	GAC
-recovered pasa_asmbl_43648.p1, terminal, 6955, 7128
-recovered pasa_asmbl_43648.p1, internal, 6491, 6739

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5865, rend_intergenic: 239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 7275
-exon list size: 54


building trellis

1.8    
3.6    
5.4    
7.1    
8.9    
10.7    
12.5    
14.3    
16.1    
17.9    
19.6    
21.4    
23.2    
25.0    
26.8    
28.6    
30.4    
32.1    
33.9    
35.7    
37.5    
39.3    
41.1    
42.9    
44.6    
46.4    
48.2    
50.0    
51.8    
53.6    
55.4    
57.1    
58.9    
60.7    
62.5    
64.3    
66.1    
67.9    
69.6    
71.4    
73.2    
75.0    
76.8    
78.6    
80.4    
82.1    
83.9    
85.7    
87.5    
89.3    
91.1    
92.9    
94.6    
96.4    
98.2    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5865, rend_intergenic: 239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support