-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_44

-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: +)
-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_61033-T1
Couldn't classify 23228, 24193
Sorry, prediction pasa_asmbl_43682.p1 fails validation.
(AGA)	 AA	23228-24193	TA	GAT
Valid prediction for GlimmerHMM_glimmerT_61034-T1
Couldn't classify 442, 625
Sorry, prediction GlimmerHMM_glimmerT_61035-T1 fails validation.
(CGT)	 AG	442-625	GT	AGG
(AGC)	 AG	1426-1524	GT	AGG
(AGC)	 AG	3094-3192	GT	AGG
(GGG)	 AG	7259-7383	GT	AGG
(AGT)	 AG	9343-9516	GT	AAG
(ATT)	 AG	10294-10453	GT	AGG
(GTC)	 AG	10653-10741	GT	TTG
(CTC)	 AG	12965-13178	CT	GAC
-recovered GlimmerHMM_glimmerT_61035-T1, terminal, 12965, 13178
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 442, 625
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 1426, 1524
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 3094, 3192
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 7259, 7383
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 9343, 9516
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 10294, 10453
-recovered GlimmerHMM_glimmerT_61035-T1, internal, 10653, 10741
Valid prediction for GlimmerHMM_glimmerT_61030-T1
Valid prediction for snap_scaffold_44-snap.4-T1
Couldn't classify 473, 631
Sorry, prediction GeneMark_model.106242_t fails validation.
(GAT)	 AG	473-631	GT	GGG
(AGC)	 AG	1426-1524	GT	AGG
(AGC)	 AG	3094-3204	CC	AAC
-recovered GeneMark_model.106242_t, terminal, 3094, 3204
-recovered GeneMark_model.106242_t, internal, 473, 631
-recovered GeneMark_model.106242_t, internal, 1426, 1524
Valid prediction for snap_scaffold_44-snap.3-T1
Valid prediction for CodingQuarry_transcript_49343-T1
Valid prediction for Augustus_model.g40597.t1
Valid prediction for GlimmerHMM_glimmerT_61032-T1
Valid prediction for snap_scaffold_44-snap.1-T1
Couldn't classify 442, 625
Sorry, prediction snap_scaffold_44-snap.5-T1 fails validation.
(CGT)	 AG	442-625	GT	AGG
(AGC)	 AG	1426-1536	CC	AAC
-recovered snap_scaffold_44-snap.5-T1, terminal, 1426, 1536
-recovered snap_scaffold_44-snap.5-T1, internal, 442, 625
Valid prediction for snap_scaffold_44-snap.2-T1
Couldn't classify 30760, 30881
Sorry, prediction GeneMark_model.106238_t fails validation.
(ATG)	 TC	30002-30015	GT	AAG
(AGA)	 AG	30601-30720	GT	GAG
(TGA)	 AG	30760-30881	GT	AGG
-recovered GeneMark_model.106238_t, initial, 30002, 30015
-recovered GeneMark_model.106238_t, terminal, 30601, 30720
-recovered GeneMark_model.106238_t, internal, 30601, 30720
-recovered GeneMark_model.106238_t, internal, 30760, 30881
Valid prediction for GlimmerHMM_glimmerT_61031-T1
Valid prediction for GeneMark_model.106239_t
Couldn't classify 7256, 7383
Sorry, prediction pasa_asmbl_43685.p1 fails validation.
(CAG)	 TC	7256-7383	GT	AGG
(AGT)	 AG	9343-9516	GT	AAG
(ATT)	 AG	10294-10453	GT	AGG
(GTC)	 AG	10653-10745	TC	AAT
-recovered pasa_asmbl_43685.p1, terminal, 10653, 10745
-recovered pasa_asmbl_43685.p1, internal, 9343, 9516
-recovered pasa_asmbl_43685.p1, internal, 10294, 10453
Couldn't classify 12876, 13178
Sorry, prediction pasa_asmbl_43684.p1 fails validation.
(CCA)	 AT	12876-13178	CT	GAC
Valid prediction for CodingQuarry_transcript_49344-T1
Valid prediction for GeneMark_model.106241_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 31495
-exon list size: 46


building trellis

2.1    
4.2    
6.2    
8.3    
10.4    
12.5    
14.6    
16.7    
18.8    
20.8    
22.9    
25.0    
27.1    
29.2    
31.2    
33.3    
35.4    
37.5    
39.6    
41.7    
43.8    
45.8    
47.9    
50.0    
52.1    
54.2    
56.2    
58.3    
60.4    
62.5    
64.6    
66.7    
68.8    
70.8    
72.9    
75.0    
77.1    
79.2    
81.2    
83.3    
85.4    
87.5    
89.6    
91.7    
93.8    
95.8    
97.9    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support