-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_2104431-2210853

-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_27-snap.488-T1
Valid prediction for GeneMark_model.101227_t
Valid prediction for CodingQuarry_transcript_41709-T1
Valid prediction for Augustus_model.g38736.t1
Valid prediction for snap_scaffold_27-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_58143-T1
Valid prediction for snap_scaffold_27-snap.499-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.512-T1
Valid prediction for pasa_asmbl_36029.p1
Valid prediction for snap_scaffold_27-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_58148-T1
Valid prediction for GeneMark_model.101217_t
Valid prediction for GlimmerHMM_glimmerT_58137-T1
Valid prediction for snap_scaffold_27-snap.493-T1
Valid prediction for snap_scaffold_27-snap.511-T1
Valid prediction for GeneMark_model.101209_t
Valid prediction for GeneMark_model.101232_t
Valid prediction for snap_scaffold_27-snap.498-T1
Valid prediction for GeneMark_model.101231_t
Valid prediction for GlimmerHMM_glimmerT_58138-T1
Valid prediction for HiQ_model.g38728.t1
Couldn't classify 21566, 21659
Sorry, prediction pasa_asmbl_36031.p1 fails validation.
(TGT)	 AA	21566-21659	GT	TTG
(CTG)	 AG	21859-22035	GT	CTG
(TCC)	 AG	22144-22224	GT	CGG
(ATG)	 AG	22435-22574	GT	AGG
(ATT)	 AG	22778-22904	GT	CAG
(ATC)	 AG	23017-23163	GT	CGG
(GTC)	 AG	23341-23436	GT	TGG
(ATA)	 AG	24002-24142	GT	AGG
(ATT)	 AG	24414-24508	GT	CGG
(AGA)	 AG	24700-24826	GT	AGG
(GCC)	 AG	25148-25283	GT	AGG
(AAG)	 AG	25610-25686	GT	AGG
(AGC)	 AG	25852-25952	GT	TGG
(AGA)	 AG	26231-26360	GT	AGG
(GTG)	 AG	26455-26504	GT	AGG
(GTT)	 AG	27731-27892	CT	AAC
add_exon() Sorry, pasa_asmbl_36031.p1 22435-22574-initial-1 is invalid.
-recovered pasa_asmbl_36031.p1, initial, 22435, 22574
add_exon() Sorry, pasa_asmbl_36031.p1 24002-24142-terminal-1 is invalid.
-recovered pasa_asmbl_36031.p1, terminal, 24002, 24142
-recovered pasa_asmbl_36031.p1, terminal, 27731, 27892
-recovered pasa_asmbl_36031.p1, internal, 21859, 22035
-recovered pasa_asmbl_36031.p1, internal, 22144, 22224
-recovered pasa_asmbl_36031.p1, internal, 22435, 22574
-recovered pasa_asmbl_36031.p1, internal, 22778, 22904
-recovered pasa_asmbl_36031.p1, internal, 23017, 23163
-recovered pasa_asmbl_36031.p1, internal, 23341, 23436
-recovered pasa_asmbl_36031.p1, internal, 24002, 24142
-recovered pasa_asmbl_36031.p1, internal, 24414, 24508
-recovered pasa_asmbl_36031.p1, internal, 24700, 24826
-recovered pasa_asmbl_36031.p1, internal, 25148, 25283
-recovered pasa_asmbl_36031.p1, internal, 25610, 25686
-recovered pasa_asmbl_36031.p1, internal, 25852, 25952
-recovered pasa_asmbl_36031.p1, internal, 26231, 26360
-recovered pasa_asmbl_36031.p1, internal, 26455, 26504
Couldn't classify 33324, 33366
Couldn't classify 34466, 34651
Sorry, prediction pasa_asmbl_36033.p1 fails validation.
(CAT)	 GC	33324-33366	GT	AGG
(AAA)	 AG	33524-33627	GT	AGG
(ATC)	 AG	34015-34123	GT	GGG
(AAC)	 AG	34228-34313	GT	GGG
(CCC)	 AG	34466-34651	TA	CCT
-recovered pasa_asmbl_36033.p1, internal, 33524, 33627
-recovered pasa_asmbl_36033.p1, internal, 34015, 34123
-recovered pasa_asmbl_36033.p1, internal, 34228, 34313
Valid prediction for Augustus_model.g38730.t1
Valid prediction for snap_scaffold_27-snap.489-T1
Valid prediction for Augustus_model.g38735.t1
Valid prediction for GeneMark_model.101215_t
Valid prediction for HiQ_model.g38725.t1
Valid prediction for snap_scaffold_27-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_58149-T1
Couldn't classify 38344, 38374
Sorry, prediction pasa_asmbl_36036.p2 fails validation.
(GGC)	 CT	38344-38374	GT	GGG
(CGC)	 AG	38573-38728	GT	CGG
(GGG)	 AG	39169-39291	GT	CCG
(CCC)	 AG	39595-39791	TC	GAT
-recovered pasa_asmbl_36036.p2, terminal, 39595, 39791
-recovered pasa_asmbl_36036.p2, internal, 38573, 38728
-recovered pasa_asmbl_36036.p2, internal, 39169, 39291
Valid prediction for GeneMark_model.101222_t
Valid prediction for Augustus_model.g38729.t1
Valid prediction for GlimmerHMM_glimmerT_58141-T1
Valid prediction for Augustus_model.g38737.t1
Valid prediction for GeneMark_model.101211_t
Valid prediction for GeneMark_model.101229_t
Valid prediction for GeneMark_model.101219_t
Valid prediction for GeneMark_model.101214_t
Valid prediction for GeneMark_model.101224_t
Valid prediction for snap_scaffold_27-snap.508-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.101225_t
Valid prediction for snap_scaffold_27-snap.502-T1
Valid prediction for snap_scaffold_27-snap.497-T1
Valid prediction for GeneMark_model.101230_t
Valid prediction for snap_scaffold_27-snap.492-T1
Valid prediction for GeneMark_model.101212_t
Valid prediction for snap_scaffold_27-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_58145-T1
Valid prediction for GeneMark_model.101210_t
Valid prediction for Augustus_model.g38727.t1
Valid prediction for GeneMark_model.101228_t
Couldn't classify 55710, 55868
Couldn't classify 56877, 56977
Sorry, prediction pasa_asmbl_36769.p2 fails validation.
(TCT)	 TC	55710-55868	GT	AGG
(CTG)	 AG	56440-56548	GT	TCG
(ACT)	 AG	56877-56977	CC	GCC
-recovered pasa_asmbl_36769.p2, internal, 56440, 56548
Valid prediction for snap_scaffold_27-snap.506-T1
Valid prediction for pasa_asmbl_36764.p1
Valid prediction for GlimmerHMM_glimmerT_58140-T1
Valid prediction for snap_scaffold_27-snap.514-T1
Valid prediction for snap_scaffold_27-snap.503-T1
Valid prediction for snap_scaffold_27-snap.507-T1
Valid prediction for snap_scaffold_27-snap.500-T1
Valid prediction for Augustus_model.g38734.t1
Valid prediction for GlimmerHMM_glimmerT_58147-T1
Valid prediction for GeneMark_model.101223_t
Valid prediction for GeneMark_model.101221_t
Valid prediction for snap_scaffold_27-snap.496-T1
Valid prediction for snap_scaffold_27-snap.501-T1
Valid prediction for GlimmerHMM_glimmerT_58139-T1
Valid prediction for GlimmerHMM_glimmerT_58144-T1
Valid prediction for GeneMark_model.101213_t
Valid prediction for GeneMark_model.101226_t
Valid prediction for Augustus_model.g38738.t1
Valid prediction for GlimmerHMM_glimmerT_58146-T1
Valid prediction for Augustus_model.g38733.t1
Valid prediction for snap_scaffold_27-snap.510-T1
Valid prediction for snap_scaffold_27-snap.490-T1
Valid prediction for snap_scaffold_27-snap.505-T1
Valid prediction for Augustus_model.g38731.t1
Valid prediction for snap_scaffold_27-snap.491-T1
Valid prediction for GeneMark_model.101218_t
Valid prediction for GeneMark_model.101220_t
Valid prediction for GlimmerHMM_glimmerT_58142-T1
Valid prediction for Augustus_model.g38732.t1
Valid prediction for GeneMark_model.101216_t
Valid prediction for snap_scaffold_27-snap.504-T1
Valid prediction for Augustus_model.g38726.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 59995, rend_intergenic: 44818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 106423
-exon list size: 399


building trellis

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81.3    
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82.3    
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83.3    
83.5    
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84.3    
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85.3    
85.5    
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86.3    
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87.3    
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88.0    
88.3    
88.5    
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89.0    
89.3    
89.5    
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90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
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95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 59995, rend_intergenic: 44818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support