-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_8207862-8611373

-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_9-snap.1719-T1
Valid prediction for GeneMark_model.39504_t
Valid prediction for snap_scaffold_9-snap.1725-T1
Valid prediction for snap_scaffold_9-snap.1721-T1
Valid prediction for GeneMark_model.39493_t
Valid prediction for snap_scaffold_9-snap.1717-T1
Valid prediction for GlimmerHMM_glimmerT_23074-T1
Valid prediction for Augustus_model.g15432.t1
Valid prediction for snap_scaffold_9-snap.1766-T1
Valid prediction for GlimmerHMM_glimmerT_23070-T1
Valid prediction for GlimmerHMM_glimmerT_23059-T1
Valid prediction for Augustus_model.g15438.t1
Valid prediction for GlimmerHMM_glimmerT_23056-T1
Valid prediction for snap_scaffold_9-snap.1735-T1
Valid prediction for CodingQuarry_transcript_62085-T1
Valid prediction for GeneMark_model.39496_t
Valid prediction for GeneMark_model.39497_t
Valid prediction for HiQ_model.g15440.t1
Valid prediction for GeneMark_model.39515_t
Couldn't classify 378914, 378937
Sorry, prediction pasa_asmbl_54165.p1 fails validation.
(ATG)	 AC	375775-375777	GT	TGG
(GTG)	 AG	375980-377869	GT	AGG
(GTG)	 AG	378914-378937	TC	TTT
-recovered pasa_asmbl_54165.p1, initial, 375775, 375777
-recovered pasa_asmbl_54165.p1, internal, 375980, 377869
Valid prediction for Augustus_model.g15429.t1
Valid prediction for GeneMark_model.39512_t
Valid prediction for Augustus_model.g15426.t1
Valid prediction for GeneMark_model.39510_t
Valid prediction for snap_scaffold_9-snap.1753-T1
Valid prediction for Augustus_model.g15455.t1
Valid prediction for snap_scaffold_9-snap.1732-T1
Valid prediction for snap_scaffold_9-snap.1728-T1
Valid prediction for snap_scaffold_9-snap.1749-T1
Valid prediction for snap_scaffold_9-snap.1752-T1
Valid prediction for Augustus_model.g15430.t1
Valid prediction for snap_scaffold_9-snap.1713-T1
Valid prediction for pasa_asmbl_54668.p1
Valid prediction for GlimmerHMM_glimmerT_23068-T1
Valid prediction for snap_scaffold_9-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_23057-T1
Valid prediction for snap_scaffold_9-snap.1747-T1
Valid prediction for pasa_asmbl_54161.p1
Valid prediction for snap_scaffold_9-snap.1711-T1
Valid prediction for GeneMark_model.39509_t
Valid prediction for snap_scaffold_9-snap.1736-T1
Valid prediction for pasa_asmbl_54148.p1
Valid prediction for snap_scaffold_9-snap.1737-T1
Valid prediction for Augustus_model.g15439.t1
Valid prediction for pasa_asmbl_54153.p1
Valid prediction for Augustus_model.g15436.t1
Valid prediction for snap_scaffold_9-snap.1758-T1
Valid prediction for Augustus_model.g15428.t1
Valid prediction for HiQ_model.g15441.t1
Valid prediction for snap_scaffold_9-snap.1730-T1
Valid prediction for Augustus_model.g15434.t1
Valid prediction for snap_scaffold_9-snap.1712-T1
Valid prediction for snap_scaffold_9-snap.1715-T1
Valid prediction for Augustus_model.g15448.t1
Valid prediction for GeneMark_model.39511_t
Valid prediction for GeneMark_model.39514_t
Valid prediction for HiQ_model.g15435.t1
Valid prediction for snap_scaffold_9-snap.1714-T1
Valid prediction for snap_scaffold_9-snap.1724-T1
Valid prediction for GeneMark_model.39508_t
Valid prediction for GeneMark_model.39525_t
Valid prediction for Augustus_model.g15447.t1
Valid prediction for Augustus_model.g15437.t1
Valid prediction for snap_scaffold_9-snap.1750-T1
Valid prediction for snap_scaffold_9-snap.1731-T1
Valid prediction for Augustus_model.g15431.t1
Valid prediction for GlimmerHMM_glimmerT_23058-T1
Valid prediction for snap_scaffold_9-snap.1726-T1
Valid prediction for GeneMark_model.39500_t
Valid prediction for GlimmerHMM_glimmerT_23055-T1
Valid prediction for GeneMark_model.39494_t
Valid prediction for GlimmerHMM_glimmerT_23052-T1
Valid prediction for Augustus_model.g15446.t1
Valid prediction for CodingQuarry_transcript_62084-T1
Valid prediction for GeneMark_model.39536_t
Valid prediction for GlimmerHMM_glimmerT_23073-T1
Valid prediction for GlimmerHMM_glimmerT_23060-T1
Valid prediction for GeneMark_model.39495_t
Valid prediction for Augustus_model.g15433.t1
Valid prediction for GeneMark_model.39519_t
Valid prediction for snap_scaffold_9-snap.1723-T1
Valid prediction for Augustus_model.g15427.t1
Valid prediction for snap_scaffold_9-snap.1727-T1
Valid prediction for snap_scaffold_9-snap.1716-T1
Valid prediction for snap_scaffold_9-snap.1738-T1
Valid prediction for GeneMark_model.39505_t
Valid prediction for GeneMark_model.39535_t
Valid prediction for GlimmerHMM_glimmerT_23063-T1
Valid prediction for GeneMark_model.39498_t
Valid prediction for snap_scaffold_9-snap.1751-T1
Valid prediction for snap_scaffold_9-snap.1720-T1
Couldn't classify 225692, 225885
Couldn't classify 226599, 226802
Sorry, prediction pasa_asmbl_54162.p1 fails validation.
(AGT)	 TA	225692-225885	GT	ACG
(GGT)	 AG	225984-226179	GT	AGG
(GAT)	 AG	226599-226802	GT	AGG
-recovered pasa_asmbl_54162.p1, internal, 225984, 226179
-recovered pasa_asmbl_54162.p1, internal, 226599, 226802
Valid prediction for snap_scaffold_9-snap.1722-T1
Valid prediction for snap_scaffold_9-snap.1767-T1
Valid prediction for GlimmerHMM_glimmerT_23051-T1
Valid prediction for GlimmerHMM_glimmerT_23064-T1
Valid prediction for GlimmerHMM_glimmerT_23053-T1
Valid prediction for GlimmerHMM_glimmerT_23065-T1
Valid prediction for snap_scaffold_9-snap.1739-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_9-snap.1755-T1
Couldn't classify 163647, 163671
Couldn't classify 166273, 166322
Sorry, prediction pasa_asmbl_55730.p1 fails validation.
(CTC)	 CT	163647-163671	GT	AGG
(GCA)	 AG	163947-164103	GT	GTG
(AGT)	 AG	164808-164870	GT	AGG
(AGA)	 AG	164972-165051	GT	TGG
(TGT)	 AG	166273-166322	AC	AGA
-recovered pasa_asmbl_55730.p1, internal, 163947, 164103
-recovered pasa_asmbl_55730.p1, internal, 164808, 164870
-recovered pasa_asmbl_55730.p1, internal, 164972, 165051
Valid prediction for GlimmerHMM_glimmerT_23066-T1
Valid prediction for snap_scaffold_9-snap.1761-T1
Valid prediction for Augustus_model.g15454.t1
Valid prediction for snap_scaffold_9-snap.1769-T1
Valid prediction for GeneMark_model.39499_t
Valid prediction for snap_scaffold_9-snap.1740-T1
Valid prediction for snap_scaffold_9-snap.1748-T1
Valid prediction for Augustus_model.g15453.t1
Valid prediction for GeneMark_model.39521_t
Valid prediction for Augustus_model.g15445.t1
Valid prediction for snap_scaffold_9-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_23054-T1
Valid prediction for GeneMark_model.39506_t
Valid prediction for Augustus_model.g15451.t1
Valid prediction for snap_scaffold_9-snap.1743-T1
Valid prediction for GeneMark_model.39518_t
Valid prediction for CodingQuarry_transcript_62089-T1
Couldn't classify 114108, 114215
Couldn't classify 114766, 114878
Sorry, prediction pasa_asmbl_55755.p1 fails validation.
(CCG)	 AG	114108-114215	GT	AAG
(GTG)	 AG	114387-114573	GT	CCG
(CTC)	 AG	114766-114878	GT	CGG
-recovered pasa_asmbl_55755.p1, internal, 114108, 114215
-recovered pasa_asmbl_55755.p1, internal, 114387, 114573
-recovered pasa_asmbl_55755.p1, internal, 114766, 114878
Valid prediction for GlimmerHMM_glimmerT_23072-T1
Valid prediction for GeneMark_model.39534_t
Valid prediction for GeneMark_model.39516_t
Valid prediction for GeneMark_model.39531_t
Valid prediction for snap_scaffold_9-snap.1765-T1
Valid prediction for snap_scaffold_9-snap.1742-T1
Valid prediction for GeneMark_model.39529_t
Valid prediction for pasa_asmbl_55102.p1
Valid prediction for GeneMark_model.39523_t
Valid prediction for snap_scaffold_9-snap.1746-T1
Valid prediction for Augustus_model.g15450.t1
Valid prediction for GeneMark_model.39513_t
Valid prediction for GeneMark_model.39501_t
Valid prediction for snap_scaffold_9-snap.1756-T1
Valid prediction for snap_scaffold_9-snap.1718-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1763-T1
Valid prediction for CodingQuarry_transcript_62086-T1
Couldn't classify 195437, 195649
Sorry, prediction pasa_asmbl_55096.p1 fails validation.
(ATG)	 TA	194301-194501	GT	AAG
(GCC)	 AG	195437-195649	TC	CTT
-recovered pasa_asmbl_55096.p1, initial, 194301, 194501
Valid prediction for GeneMark_model.39524_t
Valid prediction for HiQ_model.g15444.t1
Couldn't classify 208169, 208336
Sorry, prediction pasa_asmbl_55093.p1 fails validation.
(GCT)	 CA	208169-208336	GT	AGG
(GAG)	 AG	210229-210362	GT	AGG
(CGG)	 AG	211453-211565	GT	AGG
(GAG)	 AG	211649-211884	AG	AGA
add_exon() Sorry, pasa_asmbl_55093.p1 210229-210362-terminal-2 is invalid.
-recovered pasa_asmbl_55093.p1, terminal, 210229, 210362
-recovered pasa_asmbl_55093.p1, terminal, 211649, 211884
-recovered pasa_asmbl_55093.p1, internal, 210229, 210362
-recovered pasa_asmbl_55093.p1, internal, 211453, 211565
Valid prediction for HiQ_model.g15456.t1
Valid prediction for GeneMark_model.39526_t
Valid prediction for GeneMark_model.39533_t
Valid prediction for Augustus_model.g15452.t1
Valid prediction for GlimmerHMM_glimmerT_23075-T1
Valid prediction for GeneMark_model.39530_t
Valid prediction for snap_scaffold_9-snap.1757-T1
Couldn't classify 103848, 103922
Couldn't classify 109938, 109969
Sorry, prediction pasa_asmbl_55101.p1 fails validation.
(GCT)	 TG	103848-103922	GT	CAG
(CAG)	 AG	106207-106327	GT	AGG
(GTC)	 AG	107617-107775	GT	AGG
(ACC)	 AG	109063-109212	GT	AGG
(TGC)	 AG	109938-109969	GG	GGG
-recovered pasa_asmbl_55101.p1, internal, 106207, 106327
-recovered pasa_asmbl_55101.p1, internal, 107617, 107775
-recovered pasa_asmbl_55101.p1, internal, 109063, 109212
Valid prediction for GlimmerHMM_glimmerT_23061-T1
Valid prediction for GeneMark_model.39522_t
Valid prediction for snap_scaffold_9-snap.1759-T1
Valid prediction for GlimmerHMM_glimmerT_23069-T1
Valid prediction for snap_scaffold_9-snap.1729-T1
Valid prediction for snap_scaffold_9-snap.1745-T1
Valid prediction for snap_scaffold_9-snap.1741-T1
Valid prediction for snap_scaffold_9-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_23067-T1
Valid prediction for GeneMark_model.39532_t
Valid prediction for Augustus_model.g15443.t1
Valid prediction for snap_scaffold_9-snap.1733-T1
Valid prediction for snap_scaffold_9-snap.1768-T1
Valid prediction for GeneMark_model.39502_t
Valid prediction for GeneMark_model.39503_t
Valid prediction for GlimmerHMM_glimmerT_23062-T1
Valid prediction for snap_scaffold_9-snap.1744-T1
Valid prediction for HiQ_model.g15442.t1
Valid prediction for GeneMark_model.39527_t
Valid prediction for Augustus_model.g15449.t1
Valid prediction for snap_scaffold_9-snap.1760-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1754-T1
Valid prediction for CodingQuarry_transcript_62088-T1
Valid prediction for GlimmerHMM_glimmerT_23071-T1
Valid prediction for GeneMark_model.39528_t

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

-building trellis in range 1 - 403512
-exon list size: 542


building trellis

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41.2    
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74.6    
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76.3    
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77.0    
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78.1    
78.3    
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78.7    
78.9    
79.0    
79.2    
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79.6    
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80.0    
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80.3    
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83.3    
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84.0    
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86.0    
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86.8    
86.9    
87.1    
87.3    
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88.1    
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88.8    
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89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
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92.1    
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92.8    
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93.4    
93.6    
93.8    
93.9    
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94.5    
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95.0    
95.2    
95.4    
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95.8    
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96.1    
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97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 29755
-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 1 - 29695
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 1 - 17649
-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 3087 - 17649
	-no exons in range 17683 - 29695

-building DP trellis

-building trellis in range 380758 - 403512
-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 382873 - 403512
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 383094 - 403512
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 383094 - 395762
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 383094 - 395584
-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
	-no exons in range 383094 - 395518