-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_306

-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 GlimmerHMM_glimmerT_60167-T1
Couldn't classify 70, 214
Sorry, prediction snap_scaffold_306-snap.1-T1 fails validation.
(GTG)	 AG	70-214	GT	TGG
(GCT)	 AG	408-505	GT	CGG
(ATG)	 AG	766-909	GT	TGG
(CTG)	 AG	1233-1397	GT	AGG
(GTG)	 AG	1672-1799	GT	GGG
(ATG)	 AG	1965-2148	GT	AGG
(TCC)	 AG	2276-2363	GT	TCG
(CTC)	 AG	2741-2949	GT	ACG
(GTA)	 AG	3441-3585	GT	GAG
(AGT)	 AG	4077-4162	GT	ACG
(GTC)	 AG	4211-4324	GT	TGG
(GTG)	 AG	4656-4780	GT	AGG
(GTA)	 AG	5264-5531	TA	AAT
-recovered snap_scaffold_306-snap.1-T1, initial, 766, 909
add_exon() Sorry, snap_scaffold_306-snap.1-T1 1965-2148-initial-1 is invalid.
-recovered snap_scaffold_306-snap.1-T1, initial, 1965, 2148
-recovered snap_scaffold_306-snap.1-T1, terminal, 5264, 5531
-recovered snap_scaffold_306-snap.1-T1, internal, 70, 214
-recovered snap_scaffold_306-snap.1-T1, internal, 408, 505
-recovered snap_scaffold_306-snap.1-T1, internal, 766, 909
-recovered snap_scaffold_306-snap.1-T1, internal, 1233, 1397
-recovered snap_scaffold_306-snap.1-T1, internal, 1672, 1799
-recovered snap_scaffold_306-snap.1-T1, internal, 1965, 2148
-recovered snap_scaffold_306-snap.1-T1, internal, 2276, 2363
-recovered snap_scaffold_306-snap.1-T1, internal, 2741, 2949
-recovered snap_scaffold_306-snap.1-T1, internal, 3441, 3585
-recovered snap_scaffold_306-snap.1-T1, internal, 4077, 4162
-recovered snap_scaffold_306-snap.1-T1, internal, 4211, 4324
-recovered snap_scaffold_306-snap.1-T1, internal, 4656, 4780
Couldn't classify 70, 214
Sorry, prediction Augustus_model.g39837.t1 fails validation.
(GTG)	 AG	70-214	GT	TGG
(GCT)	 AG	408-505	GT	CGG
(ATG)	 AG	766-909	GT	TGG
(CTG)	 AG	1233-1397	GT	AGG
(GTG)	 AG	1672-1799	GT	GGG
(ATG)	 AG	1965-2148	GT	AGG
(TCC)	 AG	2276-2363	GT	TCG
(CTC)	 AG	2741-2949	GT	ACG
(GTA)	 AG	3441-3585	GT	GAG
(AGT)	 AG	4077-4324	GT	TGG
(GTG)	 AG	4656-4780	GT	AGG
(ACC)	 AG	5165-5263	GT	AGG
(GCG)	 AG	6060-6221	GT	GAG
(GGA)	 AG	6487-6649	GT	CAG
(CTC)	 AG	7214-7420	GT	CTG
(CTG)	 AG	7677-7812	GT	ACG
(GGA)	 AG	8091-8290	CC	GAC
-recovered Augustus_model.g39837.t1, initial, 766, 909
add_exon() Sorry, Augustus_model.g39837.t1 1965-2148-initial-1 is invalid.
-recovered Augustus_model.g39837.t1, initial, 1965, 2148
-recovered Augustus_model.g39837.t1, terminal, 8091, 8290
-recovered Augustus_model.g39837.t1, internal, 70, 214
-recovered Augustus_model.g39837.t1, internal, 408, 505
-recovered Augustus_model.g39837.t1, internal, 766, 909
-recovered Augustus_model.g39837.t1, internal, 1233, 1397
-recovered Augustus_model.g39837.t1, internal, 1672, 1799
-recovered Augustus_model.g39837.t1, internal, 1965, 2148
-recovered Augustus_model.g39837.t1, internal, 2276, 2363
-recovered Augustus_model.g39837.t1, internal, 2741, 2949
-recovered Augustus_model.g39837.t1, internal, 3441, 3585
-recovered Augustus_model.g39837.t1, internal, 4077, 4324
-recovered Augustus_model.g39837.t1, internal, 4656, 4780
-recovered Augustus_model.g39837.t1, internal, 5165, 5263
-recovered Augustus_model.g39837.t1, internal, 6060, 6221
-recovered Augustus_model.g39837.t1, internal, 6487, 6649
-recovered Augustus_model.g39837.t1, internal, 7214, 7420
-recovered Augustus_model.g39837.t1, internal, 7677, 7812
Couldn't classify 8091, 8234
Sorry, prediction snap_scaffold_306-snap.3-T1 fails validation.
(ATG)	 GG	5873-5883	GT	TTG
(GCG)	 AG	6060-6221	GT	GAG
(GGA)	 AG	6487-6649	GT	CAG
(CTC)	 AG	7214-7420	GT	CTG
(CTG)	 AG	7677-7812	GT	ACG
(GGA)	 AG	8091-8234	GT	GGG
-recovered snap_scaffold_306-snap.3-T1, initial, 5873, 5883
-recovered snap_scaffold_306-snap.3-T1, internal, 6060, 6221
-recovered snap_scaffold_306-snap.3-T1, internal, 6487, 6649
-recovered snap_scaffold_306-snap.3-T1, internal, 7214, 7420
-recovered snap_scaffold_306-snap.3-T1, internal, 7677, 7812
-recovered snap_scaffold_306-snap.3-T1, internal, 8091, 8234
Couldn't classify 8091, 8234
Sorry, prediction GlimmerHMM_glimmerT_60168-T1 fails validation.
(ATG)	 CC	2818-2949	GT	ACG
(GTA)	 AG	3441-3585	GT	GAG
(AGT)	 AG	4077-4324	GT	TGG
(GTG)	 AG	4656-4780	GT	AGG
(GCG)	 AG	6060-6221	GT	GAG
(GGA)	 AG	6487-6649	GT	CAG
(CTC)	 AG	7214-7420	GT	CTG
(CTG)	 AG	7677-7812	GT	ACG
(GGA)	 AG	8091-8234	GT	GGG
-recovered GlimmerHMM_glimmerT_60168-T1, initial, 2818, 2949
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 3441, 3585
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 4077, 4324
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 4656, 4780
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 6060, 6221
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 6487, 6649
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 7214, 7420
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 7677, 7812
-recovered GlimmerHMM_glimmerT_60168-T1, internal, 8091, 8234

-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_306-snap.2-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5531, rend_intergenic: 1503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7820, rend_intergenic: 5873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8318
-exon list size: 41


building trellis

2.3    
4.7    
7.0    
9.3    
11.6    
14.0    
16.3    
18.6    
20.9    
23.3    
25.6    
27.9    
30.2    
32.6    
34.9    
37.2    
39.5    
41.9    
44.2    
46.5    
48.8    
51.2    
53.5    
55.8    
58.1    
60.5    
62.8    
65.1    
67.4    
69.8    
72.1    
74.4    
76.7    
79.1    
81.4    
83.7    
86.0    
88.4    
90.7    
93.0    
95.3    
97.7    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5531, rend_intergenic: 1503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7820, rend_intergenic: 5873  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