-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_8770081-9122723

-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 snap_scaffold_3-snap.1824-T1
Valid prediction for Augustus_model.g4710.t1
Valid prediction for snap_scaffold_3-snap.1789-T1
Valid prediction for GeneMark_model.11839_t
Valid prediction for snap_scaffold_3-snap.1808-T1
Valid prediction for GeneMark_model.11857_t
Valid prediction for snap_scaffold_3-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_7157-T1
Valid prediction for Augustus_model.g4701.t1
Valid prediction for GeneMark_model.11860_t
Valid prediction for GlimmerHMM_glimmerT_7173-T1
Valid prediction for snap_scaffold_3-snap.1790-T1
Valid prediction for snap_scaffold_3-snap.1820-T1
Valid prediction for GlimmerHMM_glimmerT_7171-T1
Valid prediction for GeneMark_model.11841_t
Valid prediction for GlimmerHMM_glimmerT_7174-T1
Valid prediction for GeneMark_model.11852_t
Valid prediction for GeneMark_model.11836_t
Valid prediction for GeneMark_model.11869_t
Valid prediction for GlimmerHMM_glimmerT_7169-T1
Valid prediction for GeneMark_model.11856_t
Valid prediction for snap_scaffold_3-snap.1795-T1
Valid prediction for snap_scaffold_3-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_7172-T1
Valid prediction for GlimmerHMM_glimmerT_7160-T1
Valid prediction for snap_scaffold_3-snap.1818-T1
Valid prediction for snap_scaffold_3-snap.1821-T1
Valid prediction for snap_scaffold_3-snap.1783-T1
Valid prediction for GeneMark_model.11834_t
Valid prediction for GeneMark_model.11862_t
Valid prediction for Augustus_model.g4706.t1
Valid prediction for Augustus_model.g4705.t1
Valid prediction for GeneMark_model.11827_t
Valid prediction for GeneMark_model.11830_t
Valid prediction for snap_scaffold_3-snap.1815-T1
Valid prediction for snap_scaffold_3-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_7168-T1
Valid prediction for GeneMark_model.11840_t
Valid prediction for GeneMark_model.11843_t
Valid prediction for GeneMark_model.11826_t
Valid prediction for GeneMark_model.11831_t
Valid prediction for snap_scaffold_3-snap.1787-T1
Valid prediction for snap_scaffold_3-snap.1786-T1
Valid prediction for GeneMark_model.11865_t
Valid prediction for snap_scaffold_3-snap.1791-T1
Valid prediction for GeneMark_model.11861_t
Valid prediction for GeneMark_model.11837_t
Valid prediction for Augustus_model.g4704.t1
Valid prediction for GlimmerHMM_glimmerT_7155-T1
Valid prediction for snap_scaffold_3-snap.1822-T1
Valid prediction for GeneMark_model.11825_t
Valid prediction for GeneMark_model.11835_t
Valid prediction for snap_scaffold_3-snap.1805-T1
Valid prediction for snap_scaffold_3-snap.1806-T1
Valid prediction for Augustus_model.g4713.t1
Valid prediction for GeneMark_model.11829_t
Valid prediction for snap_scaffold_3-snap.1782-T1
Valid prediction for GeneMark_model.11824_t
Valid prediction for GeneMark_model.11845_t
Valid prediction for snap_scaffold_3-snap.1816-T1
Valid prediction for GeneMark_model.11828_t
Valid prediction for GeneMark_model.11855_t
Valid prediction for snap_scaffold_3-snap.1798-T1
Valid prediction for snap_scaffold_3-snap.1793-T1
Valid prediction for GeneMark_model.11832_t
Valid prediction for GeneMark_model.11854_t
Valid prediction for snap_scaffold_3-snap.1797-T1
Valid prediction for GlimmerHMM_glimmerT_7175-T1
Valid prediction for GeneMark_model.11868_t
Valid prediction for snap_scaffold_3-snap.1814-T1
Valid prediction for Augustus_model.g4702.t1
Valid prediction for snap_scaffold_3-snap.1810-T1
Valid prediction for CodingQuarry_transcript_46126-T1
Valid prediction for GeneMark_model.11867_t
Valid prediction for GlimmerHMM_glimmerT_7158-T1
Valid prediction for snap_scaffold_3-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_7165-T1
Valid prediction for snap_scaffold_3-snap.1812-T1
Valid prediction for snap_scaffold_3-snap.1794-T1
Valid prediction for snap_scaffold_3-snap.1788-T1
Valid prediction for HiQ_model.g4712.t1
Valid prediction for GeneMark_model.11858_t
Valid prediction for GlimmerHMM_glimmerT_7166-T1
Valid prediction for Augustus_model.g4714.t1
Valid prediction for snap_scaffold_3-snap.1784-T1
Valid prediction for GlimmerHMM_glimmerT_7161-T1
Valid prediction for snap_scaffold_3-snap.1792-T1
Valid prediction for snap_scaffold_3-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_7156-T1
Couldn't classify 272043, 272236
Sorry, prediction pasa_asmbl_40183.p1 fails validation.
(AAA)	 GA	272043-272236	GT	CGG
(GTA)	 AG	272512-272762	GT	TGG
(AGT)	 AG	272919-273063	GT	AGG
(AGG)	 AG	273256-273366	GT	ATG
(GTC)	 AG	273505-273571	GC	ATG
(ACT)	 AG	273978-274103	GC	TGG
(GCT)	 AG	274231-274411	GT	AGG
(ACC)	 AG	274790-274913	GT	AGG
(GTT)	 AG	275402-275555	CA	GAC
-recovered pasa_asmbl_40183.p1, terminal, 275402, 275555
-recovered pasa_asmbl_40183.p1, internal, 272512, 272762
-recovered pasa_asmbl_40183.p1, internal, 272919, 273063
-recovered pasa_asmbl_40183.p1, internal, 273256, 273366
-recovered pasa_asmbl_40183.p1, internal, 273505, 273571
-recovered pasa_asmbl_40183.p1, internal, 273978, 274103
-recovered pasa_asmbl_40183.p1, internal, 274231, 274411
-recovered pasa_asmbl_40183.p1, internal, 274790, 274913
Valid prediction for snap_scaffold_3-snap.1785-T1
Valid prediction for snap_scaffold_3-snap.1817-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 GeneMark_model.11864_t
Valid prediction for GeneMark_model.11859_t
Valid prediction for snap_scaffold_3-snap.1807-T1
Valid prediction for GeneMark_model.11849_t
Valid prediction for GlimmerHMM_glimmerT_7162-T1
Valid prediction for GeneMark_model.11842_t
Valid prediction for GeneMark_model.11846_t
Valid prediction for HiQ_model.g4708.t1
Valid prediction for snap_scaffold_3-snap.1823-T1
Valid prediction for snap_scaffold_3-snap.1802-T1
Valid prediction for snap_scaffold_3-snap.1780-T1
Valid prediction for snap_scaffold_3-snap.1809-T1
Valid prediction for GeneMark_model.11850_t
Valid prediction for snap_scaffold_3-snap.1825-T1
Valid prediction for GeneMark_model.11863_t
Valid prediction for GlimmerHMM_glimmerT_7154-T1
Valid prediction for GeneMark_model.11833_t
Valid prediction for HiQ_model.g4707.t1
Valid prediction for snap_scaffold_3-snap.1800-T1
Valid prediction for snap_scaffold_3-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_7163-T1
Valid prediction for GlimmerHMM_glimmerT_7164-T1
Valid prediction for snap_scaffold_3-snap.1801-T1
Valid prediction for GeneMark_model.11853_t
Valid prediction for GeneMark_model.11866_t
Valid prediction for GeneMark_model.11848_t
Valid prediction for GeneMark_model.11844_t
Valid prediction for snap_scaffold_3-snap.1799-T1
Valid prediction for GeneMark_model.11851_t
Couldn't classify 104479, 104572
Sorry, prediction pasa_asmbl_39006.p1 fails validation.
(TAT)	 GC	104479-104572	GT	CGG
(AGG)	 AG	106993-107097	GT	AGG
(CTT)	 AG	108351-108397	GT	TTG
(GGA)	 AG	110651-110714	GT	TTG
(ACC)	 AG	112912-113010	GT	GAG
(AGA)	 AG	113421-113524	GT	GGG
(AAC)	 AG	114583-114730	GT	TGG
(ACC)	 AG	115896-116014	GT	AGG
(GCA)	 AG	117089-117175	GT	AGG
(GCT)	 AG	117283-117348	GT	AGG
(GAC)	 AG	119006-119110	GT	AGG
(GAC)	 AG	120256-120318	GT	ATG
(AAC)	 AG	120619-120819	GT	AGG
(GTA)	 AG	121366-121592	GT	AGG
(GTG)	 AG	121725-121925	GT	AGG
(GGA)	 AG	123211-123304	GT	CGG
(CTG)	 AG	124019-124168	GT	CGG
(CAA)	 AG	124273-124341	GT	AGG
(GCT)	 AG	124459-124545	GT	AGG
(GCG)	 AG	124934-125020	GT	AGG
(GCT)	 AG	127333-127419	GT	AGG
(GTC)	 AG	128431-128505	GT	TTG
(ATG)	 AG	128661-128795	GT	GGG
(TGC)	 AG	128928-129034	GT	AGG
(TGT)	 AG	129157-129289	GT	AGG
(GGT)	 AG	129570-129722	GT	AGG
(GGC)	 AG	129912-130042	GT	GAG
(GTT)	 AG	130158-130287	AG	AAA
-recovered pasa_asmbl_39006.p1, initial, 128661, 128795
add_exon() Sorry, pasa_asmbl_39006.p1 112912-113010-terminal-1 is invalid.
-recovered pasa_asmbl_39006.p1, terminal, 112912, 113010
add_exon() Sorry, pasa_asmbl_39006.p1 121725-121925-terminal-1 is invalid.
-recovered pasa_asmbl_39006.p1, terminal, 121725, 121925
-recovered pasa_asmbl_39006.p1, terminal, 130158, 130287
-recovered pasa_asmbl_39006.p1, internal, 106993, 107097
-recovered pasa_asmbl_39006.p1, internal, 108351, 108397
-recovered pasa_asmbl_39006.p1, internal, 110651, 110714
-recovered pasa_asmbl_39006.p1, internal, 112912, 113010
-recovered pasa_asmbl_39006.p1, internal, 113421, 113524
-recovered pasa_asmbl_39006.p1, internal, 114583, 114730
-recovered pasa_asmbl_39006.p1, internal, 115896, 116014
-recovered pasa_asmbl_39006.p1, internal, 117089, 117175
-recovered pasa_asmbl_39006.p1, internal, 117283, 117348
-recovered pasa_asmbl_39006.p1, internal, 119006, 119110
-recovered pasa_asmbl_39006.p1, internal, 120256, 120318
-recovered pasa_asmbl_39006.p1, internal, 120619, 120819
-recovered pasa_asmbl_39006.p1, internal, 121366, 121592
-recovered pasa_asmbl_39006.p1, internal, 121725, 121925
-recovered pasa_asmbl_39006.p1, internal, 123211, 123304
-recovered pasa_asmbl_39006.p1, internal, 124019, 124168
-recovered pasa_asmbl_39006.p1, internal, 124273, 124341
-recovered pasa_asmbl_39006.p1, internal, 124459, 124545
-recovered pasa_asmbl_39006.p1, internal, 124934, 125020
-recovered pasa_asmbl_39006.p1, internal, 127333, 127419
-recovered pasa_asmbl_39006.p1, internal, 128431, 128505
-recovered pasa_asmbl_39006.p1, internal, 128661, 128795
-recovered pasa_asmbl_39006.p1, internal, 128928, 129034
-recovered pasa_asmbl_39006.p1, internal, 129157, 129289
-recovered pasa_asmbl_39006.p1, internal, 129570, 129722
-recovered pasa_asmbl_39006.p1, internal, 129912, 130042
Valid prediction for GlimmerHMM_glimmerT_7167-T1
Valid prediction for GeneMark_model.11838_t
Valid prediction for pasa_asmbl_39000.p1
Valid prediction for GeneMark_model.11870_t
Valid prediction for GlimmerHMM_glimmerT_7159-T1
Valid prediction for GlimmerHMM_glimmerT_7176-T1
Valid prediction for Augustus_model.g4709.t1
Valid prediction for snap_scaffold_3-snap.1803-T1
Valid prediction for Augustus_model.g4703.t1
Valid prediction for Augustus_model.g4715.t1
Valid prediction for CodingQuarry_transcript_46125-T1
Valid prediction for pasa_asmbl_39002.p1
Valid prediction for Augustus_model.g4711.t1
Valid prediction for GlimmerHMM_glimmerT_7170-T1

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

-building trellis in range 1 - 352643
-exon list size: 598


building trellis

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78.0    
78.2    
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78.8    
79.0    
79.2    
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80.8    
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81.8    
82.0    
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82.8    
83.0    
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93.0    
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93.3    
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93.7    
93.8    
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95.3    
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95.8    
96.0    
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96.7    
96.8    
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97.8    
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98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
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99.7    
99.8    
-found 27 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 48719
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
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24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 40925
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 32813
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 31791
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 19414
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1140 - 19414
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1140 - 16767
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1140 - 12217
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1257 - 12217

-building DP trellis

-building trellis in range 19460 - 31791
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 21590 - 31791
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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