-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_12311537-12526609

-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_37933-T1
Valid prediction for CodingQuarry_transcript_18128-T1
Valid prediction for GeneMark_model.65214_t
Valid prediction for snap_scaffold_15-snap.2523-T1
Valid prediction for snap_scaffold_15-snap.2528-T1
Valid prediction for GlimmerHMM_glimmerT_37915-T1
Valid prediction for GeneMark_model.65215_t
Valid prediction for GeneMark_model.65223_t
Valid prediction for GeneMark_model.65246_t
Valid prediction for HiQ_model.g25415.t1
Valid prediction for GlimmerHMM_glimmerT_37921-T1
Valid prediction for HiQ_model.g25421.t1
Valid prediction for GlimmerHMM_glimmerT_37929-T1
Valid prediction for snap_scaffold_15-snap.2513-T1
Valid prediction for GlimmerHMM_glimmerT_37932-T1
Valid prediction for HiQ_model.g25422.t1
Valid prediction for GeneMark_model.65240_t
Valid prediction for HiQ_model.g25429.t1
Valid prediction for pasa_asmbl_14501.p2
Valid prediction for GeneMark_model.65219_t
Valid prediction for Augustus_model.g25414.t1
Valid prediction for pasa_asmbl_14509.p1
Valid prediction for Augustus_model.g25426.t1
Valid prediction for snap_scaffold_15-snap.2519-T1
Valid prediction for Augustus_model.g25424.t1
Valid prediction for CodingQuarry_transcript_18130-T1
Valid prediction for snap_scaffold_15-snap.2525-T1
Valid prediction for snap_scaffold_15-snap.2516-T1
Valid prediction for pasa_asmbl_14494.p1
Valid prediction for pasa_asmbl_14515.p1
Valid prediction for GlimmerHMM_glimmerT_37922-T1
Valid prediction for GeneMark_model.65230_t
Valid prediction for pasa_asmbl_14496.p1
Valid prediction for GeneMark_model.65233_t
Valid prediction for GlimmerHMM_glimmerT_37919-T1
Valid prediction for GeneMark_model.65212_t
Valid prediction for GeneMark_model.65221_t
Valid prediction for snap_scaffold_15-snap.2529-T1
Valid prediction for GeneMark_model.65234_t
Valid prediction for GeneMark_model.65229_t
Valid prediction for snap_scaffold_15-snap.2532-T1
Valid prediction for Augustus_model.g25423.t1
Valid prediction for GlimmerHMM_glimmerT_37923-T1
Valid prediction for GlimmerHMM_glimmerT_37918-T1
Valid prediction for snap_scaffold_15-snap.2533-T1
Valid prediction for snap_scaffold_15-snap.2527-T1
Valid prediction for GeneMark_model.65231_t
Valid prediction for GeneMark_model.65227_t
Valid prediction for GlimmerHMM_glimmerT_37934-T1
Valid prediction for pasa_asmbl_14519.p1
Valid prediction for GeneMark_model.65238_t
Couldn't classify 207502, 207711
Couldn't classify 214302, 214655
Sorry, prediction pasa_asmbl_14520.p1 fails validation.
(GGC)	 CA	207502-207711	GT	AGG
(GCG)	 AG	209339-209414	GT	AGG
(AGC)	 AG	210284-210444	GT	CGG
(ATG)	 AG	210660-210803	GT	AGG
(TCG)	 AG	211095-211284	GT	AGG
(TGC)	 AG	212948-213126	GT	AGG
(AAC)	 AG	213720-214133	GT	GGG
(AAC)	 AG	214302-214655	GA	CCG
-recovered pasa_asmbl_14520.p1, initial, 210660, 210803
-recovered pasa_asmbl_14520.p1, internal, 209339, 209414
-recovered pasa_asmbl_14520.p1, internal, 210284, 210444
-recovered pasa_asmbl_14520.p1, internal, 210660, 210803
-recovered pasa_asmbl_14520.p1, internal, 211095, 211284
-recovered pasa_asmbl_14520.p1, internal, 212948, 213126
-recovered pasa_asmbl_14520.p1, internal, 213720, 214133
Valid prediction for CodingQuarry_transcript_18129-T1
Valid prediction for snap_scaffold_15-snap.2535-T1
Valid prediction for GlimmerHMM_glimmerT_37907-T1
Valid prediction for GlimmerHMM_glimmerT_37910-T1
Valid prediction for snap_scaffold_15-snap.2536-T1
Valid prediction for GeneMark_model.65244_t
Valid prediction for GeneMark_model.65225_t
Valid prediction for Augustus_model.g25417.t1
Valid prediction for CodingQuarry_transcript_18131-T1
Valid prediction for GeneMark_model.65232_t
Valid prediction for GeneMark_model.65241_t
Valid prediction for HiQ_model.g25419.t1
Valid prediction for CodingQuarry_transcript_18126-T1
Valid prediction for GlimmerHMM_glimmerT_37908-T1
Valid prediction for snap_scaffold_15-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_37912-T1
Valid prediction for GlimmerHMM_glimmerT_37925-T1
Valid prediction for Augustus_model.g25425.t1
Valid prediction for snap_scaffold_15-snap.2530-T1
Valid prediction for GeneMark_model.65242_t
Valid prediction for snap_scaffold_15-snap.2537-T1
Valid prediction for GeneMark_model.65237_t
Valid prediction for HiQ_model.g25428.t1
Valid prediction for GlimmerHMM_glimmerT_37920-T1
Valid prediction for snap_scaffold_15-snap.2524-T1
Valid prediction for GeneMark_model.65236_t
Valid prediction for snap_scaffold_15-snap.2526-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 GlimmerHMM_glimmerT_37911-T1
Valid prediction for Augustus_model.g25420.t1
Valid prediction for GlimmerHMM_glimmerT_37913-T1
Valid prediction for snap_scaffold_15-snap.2511-T1
Valid prediction for GlimmerHMM_glimmerT_37906-T1
Valid prediction for snap_scaffold_15-snap.2508-T1
Valid prediction for GlimmerHMM_glimmerT_37909-T1
Valid prediction for GlimmerHMM_glimmerT_37904-T1
Valid prediction for GeneMark_model.65220_t
Valid prediction for snap_scaffold_15-snap.2514-T1
Valid prediction for GlimmerHMM_glimmerT_37928-T1
Valid prediction for GeneMark_model.65211_t
Valid prediction for Augustus_model.g25413.t1
Valid prediction for Augustus_model.g25410.t1
Valid prediction for Augustus_model.g25418.t1
Valid prediction for GlimmerHMM_glimmerT_37930-T1
Valid prediction for GlimmerHMM_glimmerT_37926-T1
Valid prediction for GeneMark_model.65228_t
Valid prediction for GlimmerHMM_glimmerT_37924-T1
Valid prediction for GeneMark_model.65216_t
Valid prediction for GlimmerHMM_glimmerT_37914-T1
Valid prediction for Augustus_model.g25416.t1
Valid prediction for snap_scaffold_15-snap.2517-T1
Couldn't classify 128443, 128526
Sorry, prediction pasa_asmbl_15588.p1 fails validation.
(GTG)	 AG	128443-128526	GT	AGG
(CAG)	 AG	129459-129641	GT	CCG
(AAT)	 AG	129895-130000	GT	AGG
(AGC)	 AG	130907-131054	GT	AGG
(GTA)	 AG	131485-131629	GT	AGG
(ACA)	 AG	132475-132513	GT	CAG
(TAC)	 AG	132872-132943	GT	TGG
(GAA)	 AG	133718-133781	GT	ACG
(GCA)	 AG	133924-134004	GT	TGG
(GCA)	 AG	134344-134434	GT	CTG
(AAA)	 AG	134530-134591	GT	CGG
(ACG)	 AG	134708-135056	GT	ATG
(GCA)	 AG	135563-135593	GC	GAG
-recovered pasa_asmbl_15588.p1, terminal, 135563, 135593
-recovered pasa_asmbl_15588.p1, internal, 128443, 128526
-recovered pasa_asmbl_15588.p1, internal, 129459, 129641
-recovered pasa_asmbl_15588.p1, internal, 129895, 130000
-recovered pasa_asmbl_15588.p1, internal, 130907, 131054
-recovered pasa_asmbl_15588.p1, internal, 131485, 131629
-recovered pasa_asmbl_15588.p1, internal, 132475, 132513
-recovered pasa_asmbl_15588.p1, internal, 132872, 132943
-recovered pasa_asmbl_15588.p1, internal, 133718, 133781
-recovered pasa_asmbl_15588.p1, internal, 133924, 134004
-recovered pasa_asmbl_15588.p1, internal, 134344, 134434
-recovered pasa_asmbl_15588.p1, internal, 134530, 134591
-recovered pasa_asmbl_15588.p1, internal, 134708, 135056
-recovered pasa_asmbl_15588.p1, internal, 135563, 135593
Valid prediction for snap_scaffold_15-snap.2509-T1
Valid prediction for snap_scaffold_15-snap.2510-T1
Valid prediction for GlimmerHMM_glimmerT_37931-T1
Valid prediction for Augustus_model.g25411.t1
Valid prediction for GeneMark_model.65217_t
Valid prediction for HiQ_model.g25427.t1
Valid prediction for GeneMark_model.65239_t
Valid prediction for snap_scaffold_15-snap.2522-T1
Valid prediction for Augustus_model.g25412.t1
Valid prediction for snap_scaffold_15-snap.2521-T1
Valid prediction for snap_scaffold_15-snap.2507-T1
Valid prediction for GlimmerHMM_glimmerT_37916-T1
Valid prediction for snap_scaffold_15-snap.2512-T1
Valid prediction for GlimmerHMM_glimmerT_37917-T1
Valid prediction for GlimmerHMM_glimmerT_37927-T1
Valid prediction for GeneMark_model.65224_t
Valid prediction for GlimmerHMM_glimmerT_37905-T1
Valid prediction for GeneMark_model.65243_t
Valid prediction for GeneMark_model.65213_t
Valid prediction for GeneMark_model.65226_t
Valid prediction for snap_scaffold_15-snap.2520-T1
Couldn't classify 119562, 119720
Couldn't classify 126657, 126686
Sorry, prediction pasa_asmbl_15594.p1 fails validation.
(AAC)	 AC	119562-119720	GT	GGG
(GAA)	 AG	120045-120192	GT	AGG
(TAG)	 AG	120554-120627	GT	AGG
(ATT)	 AG	120831-120937	GT	ATG
(AGT)	 AG	121113-121220	GT	GGG
(GTT)	 AG	122166-122287	GT	TGG
(ACG)	 AG	123576-123698	GT	CGG
(CCT)	 AG	124045-124208	GT	CCG
(GCC)	 AG	126218-126337	GT	AGG
(ATT)	 AG	126657-126686	TT	ATT
-recovered pasa_asmbl_15594.p1, internal, 120045, 120192
-recovered pasa_asmbl_15594.p1, internal, 120554, 120627
-recovered pasa_asmbl_15594.p1, internal, 120831, 120937
-recovered pasa_asmbl_15594.p1, internal, 121113, 121220
-recovered pasa_asmbl_15594.p1, internal, 122166, 122287
-recovered pasa_asmbl_15594.p1, internal, 123576, 123698
-recovered pasa_asmbl_15594.p1, internal, 124045, 124208
-recovered pasa_asmbl_15594.p1, internal, 126218, 126337
Valid prediction for GeneMark_model.65235_t
Valid prediction for GeneMark_model.65245_t
Valid prediction for snap_scaffold_15-snap.2531-T1
Valid prediction for snap_scaffold_15-snap.2518-T1
Couldn't classify 171104, 171142
Couldn't classify 171832, 172055
Sorry, prediction pasa_asmbl_15956.p1 fails validation.
(TCC)	 CC	171104-171142	GT	AGG
(CTT)	 AG	171393-171432	GT	AGG
(GCG)	 AG	171562-171657	GT	AGG
(ACC)	 AG	171832-172055	GG	TGG
add_exon() Sorry, pasa_asmbl_15956.p1 171562-171657-terminal-1 is invalid.
-recovered pasa_asmbl_15956.p1, terminal, 171562, 171657
-recovered pasa_asmbl_15956.p1, internal, 171393, 171432
-recovered pasa_asmbl_15956.p1, internal, 171562, 171657
Valid prediction for CodingQuarry_transcript_18132-T1
Valid prediction for GeneMark_model.65222_t
Valid prediction for snap_scaffold_15-snap.2515-T1

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

-building trellis in range 1 - 215073
-exon list size: 466


building trellis

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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12582
-exon list size: 15


building trellis

5.9    
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41.2    
47.1    
52.9    
58.8    
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70.6    
76.5    
82.4    
88.2    
94.1    
-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