-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_15311063-15535203

-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 pasa_asmbl_15794.p1
Couldn't classify 34624, 34755
Couldn't classify 36928, 36977
Sorry, prediction pasa_asmbl_15754.p1 fails validation.
(CGT)	 AT	34624-34755	GT	ACG
(ATT)	 AG	36730-36853	GT	AGG
(GGC)	 AG	36928-36977	CC	GAC
-recovered pasa_asmbl_15754.p1, internal, 36730, 36853
Valid prediction for Augustus_model.g25010.t1
Couldn't classify 98536, 98738
Sorry, prediction pasa_asmbl_15770.p1 fails validation.
(CCC)	 TT	98536-98738	GT	TTG
(GTA)	 AG	98842-98930	GT	GGG
(CAG)	 AG	99121-99143	CT	AGC
-recovered pasa_asmbl_15770.p1, terminal, 99121, 99143
-recovered pasa_asmbl_15770.p1, internal, 98842, 98930
Valid prediction for snap_scaffold_15-snap.3053-T1
Valid prediction for GlimmerHMM_glimmerT_37491-T1
Valid prediction for snap_scaffold_15-snap.3052-T1
Valid prediction for snap_scaffold_15-snap.3049-T1
Valid prediction for Augustus_model.g24993.t1
Valid prediction for GlimmerHMM_glimmerT_37511-T1
Valid prediction for GlimmerHMM_glimmerT_37513-T1
Valid prediction for snap_scaffold_15-snap.3041-T1
Valid prediction for GlimmerHMM_glimmerT_37495-T1
Valid prediction for pasa_asmbl_15783.p2
Valid prediction for Augustus_model.g24995.t1
Couldn't classify 89370, 89617
Sorry, prediction pasa_asmbl_15765.p1 fails validation.
(CCC)	 TC	89370-89617	GT	AGG
(GCG)	 AG	89756-90074	CT	GAC
-recovered pasa_asmbl_15765.p1, terminal, 89756, 90074
Valid prediction for snap_scaffold_15-snap.3037-T1
Valid prediction for CodingQuarry_transcript_18261-T1
Valid prediction for snap_scaffold_15-snap.3038-T1
Valid prediction for GlimmerHMM_glimmerT_37503-T1
Valid prediction for snap_scaffold_15-snap.3057-T1
Valid prediction for Augustus_model.g25000.t1
Valid prediction for HiQ_model.g24988.t1
Valid prediction for snap_scaffold_15-snap.3054-T1
Valid prediction for GlimmerHMM_glimmerT_37514-T1
Valid prediction for snap_scaffold_15-snap.3040-T1
Valid prediction for GlimmerHMM_glimmerT_37519-T1
Valid prediction for snap_scaffold_15-snap.3071-T1
Valid prediction for Augustus_model.g25002.t1
Valid prediction for snap_scaffold_15-snap.3044-T1
Valid prediction for GlimmerHMM_glimmerT_37509-T1
Valid prediction for HiQ_model.g24991.t1
Valid prediction for CodingQuarry_transcript_18254-T1
Valid prediction for Augustus_model.g24992.t1
Valid prediction for GlimmerHMM_glimmerT_37488-T1
Valid prediction for snap_scaffold_15-snap.3055-T1
Valid prediction for pasa_asmbl_15799.p1
Couldn't classify 86061, 86120
Couldn't classify 88959, 89120
Sorry, prediction pasa_asmbl_15764.p1 fails validation.
(GTA)	 AC	86061-86120	GT	AGG
(GTG)	 AG	87287-87501	GT	TAG
(TCT)	 AG	88467-88851	GT	AGG
(TCT)	 AG	88959-89120	CC	CCC
-recovered pasa_asmbl_15764.p1, internal, 87287, 87501
-recovered pasa_asmbl_15764.p1, internal, 88467, 88851
Valid prediction for Augustus_model.g25004.t1
Valid prediction for snap_scaffold_15-snap.3067-T1
Valid prediction for HiQ_model.g25007.t1
Valid prediction for Augustus_model.g25013.t1
Valid prediction for pasa_asmbl_15748.p1
Valid prediction for GlimmerHMM_glimmerT_37504-T1
Valid prediction for snap_scaffold_15-snap.3051-T1
Valid prediction for HiQ_model.g25015.t1
Valid prediction for snap_scaffold_15-snap.3070-T1
Valid prediction for Augustus_model.g24989.t1
Valid prediction for GlimmerHMM_glimmerT_37492-T1
Valid prediction for snap_scaffold_15-snap.3036-T1
Valid prediction for pasa_asmbl_15798.p1
Valid prediction for snap_scaffold_15-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_37500-T1
Valid prediction for snap_scaffold_15-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_37507-T1
Valid prediction for Augustus_model.g25014.t1
Valid prediction for snap_scaffold_15-snap.3063-T1
Valid prediction for GlimmerHMM_glimmerT_37499-T1
Valid prediction for CodingQuarry_transcript_18255-T1
Valid prediction for GlimmerHMM_glimmerT_37515-T1
Valid prediction for GlimmerHMM_glimmerT_37501-T1
Valid prediction for CodingQuarry_transcript_18262-T1
Valid prediction for CodingQuarry_transcript_18259-T1
Valid prediction for GlimmerHMM_glimmerT_37490-T1

-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_15-snap.3064-T1
Valid prediction for GlimmerHMM_glimmerT_37505-T1
Valid prediction for snap_scaffold_15-snap.3075-T1
Valid prediction for GlimmerHMM_glimmerT_37508-T1
Valid prediction for Augustus_model.g25012.t1
Valid prediction for snap_scaffold_15-snap.3042-T1
Valid prediction for HiQ_model.g25017.t1
Valid prediction for HiQ_model.g25005.t1
Valid prediction for snap_scaffold_15-snap.3072-T1
Valid prediction for snap_scaffold_15-snap.3046-T1
Valid prediction for pasa_asmbl_14778.p2
Valid prediction for Augustus_model.g25003.t1
Valid prediction for snap_scaffold_15-snap.3059-T1
Valid prediction for GlimmerHMM_glimmerT_37512-T1
Valid prediction for GlimmerHMM_glimmerT_37510-T1
Valid prediction for snap_scaffold_15-snap.3068-T1
Valid prediction for Augustus_model.g25001.t1
Valid prediction for Augustus_model.g24994.t1
Couldn't classify 179753, 179865
Couldn't classify 180363, 180418
Sorry, prediction pasa_asmbl_14767.p1 fails validation.
(GTG)	 AG	179753-179865	GT	GGG
(CTG)	 AG	179953-180091	GT	TGG
(GTA)	 AG	180206-180296	GT	AGG
(GTC)	 AG	180363-180418	AT	CCA
-recovered pasa_asmbl_14767.p1, internal, 179753, 179865
-recovered pasa_asmbl_14767.p1, internal, 179953, 180091
-recovered pasa_asmbl_14767.p1, internal, 180206, 180296
Valid prediction for snap_scaffold_15-snap.3045-T1
Valid prediction for snap_scaffold_15-snap.3060-T1
Valid prediction for Augustus_model.g25019.t1
Valid prediction for GlimmerHMM_glimmerT_37496-T1
Valid prediction for Augustus_model.g25018.t1
Couldn't classify 153671, 153868
Sorry, prediction pasa_asmbl_14768.p1 fails validation.
(CAT)	 CC	153671-153868	GT	AGG
(GAT)	 AG	154156-154501	GT	TTG
(GCA)	 AG	154919-154985	GT	CCG
(GCG)	 AG	155238-155380	GT	AGG
(TGG)	 AG	155467-155570	GT	TTG
(GAG)	 AG	155693-155768	GT	AGG
(GGT)	 AG	156864-156952	GT	TGG
(GTG)	 AG	157048-157191	GT	AGG
(AAC)	 AG	157299-157415	GT	ACG
(ACT)	 AG	157546-157712	GT	AGG
(AGT)	 AG	159925-160192	AA	GAA
add_exon() Sorry, pasa_asmbl_14768.p1 157546-157712-terminal-2 is invalid.
-recovered pasa_asmbl_14768.p1, terminal, 157546, 157712
-recovered pasa_asmbl_14768.p1, terminal, 159925, 160192
-recovered pasa_asmbl_14768.p1, internal, 154156, 154501
-recovered pasa_asmbl_14768.p1, internal, 154919, 154985
-recovered pasa_asmbl_14768.p1, internal, 155238, 155380
-recovered pasa_asmbl_14768.p1, internal, 155467, 155570
-recovered pasa_asmbl_14768.p1, internal, 155693, 155768
-recovered pasa_asmbl_14768.p1, internal, 156864, 156952
-recovered pasa_asmbl_14768.p1, internal, 157048, 157191
-recovered pasa_asmbl_14768.p1, internal, 157299, 157415
-recovered pasa_asmbl_14768.p1, internal, 157546, 157712
Valid prediction for snap_scaffold_15-snap.3069-T1
Valid prediction for snap_scaffold_15-snap.3062-T1
Couldn't classify 145715, 146809
Sorry, prediction pasa_asmbl_14770.p1 fails validation.
(GCT)	 GA	145715-146809	GT	AGG
Couldn't classify 110896, 111192
Sorry, prediction pasa_asmbl_14781.p1 fails validation.
(ATG)	 AA	110896-111192	TA	AGT
Valid prediction for Augustus_model.g25008.t1
Valid prediction for GlimmerHMM_glimmerT_37520-T1
Couldn't classify 8833, 8928
Couldn't classify 9430, 9473
Sorry, prediction pasa_asmbl_14900.p1 fails validation.
(CTG)	 AA	8833-8928	GT	AGG
(GAC)	 AG	9111-9339	GT	ACG
(AGA)	 AG	9430-9473	AG	AGA
-recovered pasa_asmbl_14900.p1, internal, 9111, 9339
Valid prediction for GlimmerHMM_glimmerT_37502-T1
Valid prediction for snap_scaffold_15-snap.3043-T1
Valid prediction for snap_scaffold_15-snap.3047-T1
Valid prediction for snap_scaffold_15-snap.3050-T1
Valid prediction for snap_scaffold_15-snap.3061-T1
Valid prediction for GlimmerHMM_glimmerT_37518-T1
Valid prediction for CodingQuarry_transcript_18258-T1
Valid prediction for snap_scaffold_15-snap.3065-T1
Valid prediction for snap_scaffold_15-snap.3073-T1
Valid prediction for GlimmerHMM_glimmerT_37517-T1
Valid prediction for GlimmerHMM_glimmerT_37497-T1
Valid prediction for snap_scaffold_15-snap.3048-T1
Valid prediction for Augustus_model.g25016.t1
Couldn't classify 13953, 14330
Sorry, prediction pasa_asmbl_14790.p1 fails validation.
(CAC)	 CC	13953-14330	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_37516-T1
Valid prediction for GlimmerHMM_glimmerT_37506-T1
Valid prediction for Augustus_model.g24990.t1
Valid prediction for snap_scaffold_15-snap.3076-T1
Valid prediction for snap_scaffold_15-snap.3074-T1
Valid prediction for snap_scaffold_15-snap.3058-T1
Couldn't classify 151269, 151640
Sorry, prediction pasa_asmbl_15763.p1 fails validation.
(ATG)	 AG	151269-151640	GA	GAG
Valid prediction for Augustus_model.g25009.t1
Valid prediction for HiQ_model.g25006.t1
Valid prediction for GlimmerHMM_glimmerT_37489-T1
Valid prediction for GlimmerHMM_glimmerT_37493-T1
Valid prediction for Augustus_model.g24999.t1
Valid prediction for Augustus_model.g24997.t1
Valid prediction for HiQ_model.g24996.t1
Valid prediction for snap_scaffold_15-snap.3066-T1
Couldn't classify 110397, 110565
Couldn't classify 110979, 111191
Sorry, prediction CodingQuarry_transcript_18257-T1 fails validation.
(ATG)	 CA	103736-103990	GT	CGG
(GAA)	 AG	106264-106333	GT	TGG
(GTG)	 AG	106969-107087	GT	AGG
(TTC)	 AG	107312-107445	GT	AAG
(GTT)	 AG	107522-107690	GT	ATG
(GTG)	 AG	108081-108161	GT	AGG
(TGT)	 AG	109453-109544	GT	AAG
(AGC)	 AG	109663-109740	GT	TGG
(GAT)	 AG	109894-110054	GT	AGG
(ACA)	 AG	110397-110565	AT	TCA
(GCA)	 CT	110979-111191	GT	GAG
(GGA)	 AG	111432-111468	GT	TGG
(CCA)	 AG	112358-112453	GT	AGG
(CCC)	 AG	113007-113081	GT	ATG
(GAT)	 AG	113207-113264	GT	ATG
(ATA)	 AG	113340-113404	GT	ATG
(ACA)	 AG	113601-113756	TA	GAT
-recovered CodingQuarry_transcript_18257-T1, initial, 103736, 103990
-recovered CodingQuarry_transcript_18257-T1, terminal, 113601, 113756
-recovered CodingQuarry_transcript_18257-T1, internal, 106264, 106333
-recovered CodingQuarry_transcript_18257-T1, internal, 106969, 107087
-recovered CodingQuarry_transcript_18257-T1, internal, 107312, 107445
-recovered CodingQuarry_transcript_18257-T1, internal, 107522, 107690
-recovered CodingQuarry_transcript_18257-T1, internal, 108081, 108161
-recovered CodingQuarry_transcript_18257-T1, internal, 109453, 109544
-recovered CodingQuarry_transcript_18257-T1, internal, 109663, 109740
-recovered CodingQuarry_transcript_18257-T1, internal, 109894, 110054
-recovered CodingQuarry_transcript_18257-T1, internal, 111432, 111468
-recovered CodingQuarry_transcript_18257-T1, internal, 112358, 112453
-recovered CodingQuarry_transcript_18257-T1, internal, 113007, 113081
-recovered CodingQuarry_transcript_18257-T1, internal, 113207, 113264
-recovered CodingQuarry_transcript_18257-T1, internal, 113340, 113404
Valid prediction for Augustus_model.g25011.t1
Valid prediction for Augustus_model.g24998.t1
Valid prediction for GlimmerHMM_glimmerT_37498-T1
Valid prediction for GlimmerHMM_glimmerT_37494-T1

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

-building trellis in range 1 - 224141
-exon list size: 380


building trellis

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14.7    
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17.5    
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18.1    
18.3    
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18.8    
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19.9    
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22.3    
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22.8    
23.0    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
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44.0    
44.2    
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44.8    
45.0    
45.3    
45.5    
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46.1    
46.3    
46.6    
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47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
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50.0    
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50.5    
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51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
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52.9    
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56.3    
56.5    
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57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
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62.3    
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62.8    
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63.4    
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63.9    
64.1    
64.4    
64.7    
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65.4    
65.7    
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66.2    
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67.0    
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68.1    
68.3    
68.6    
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69.6    
69.9    
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73.0    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
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77.0    
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78.0    
78.3    
78.5    
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79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
81.9    
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82.5    
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83.0    
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84.0    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
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87.7    
88.0    
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89.0    
89.3    
89.5    
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90.1    
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90.6    
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91.4    
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91.9    
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97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support