-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_641

-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 GeneMark_model.108109_t
Valid prediction for GeneMark_model.108108_t
Valid prediction for GeneMark_model.108110_t

-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: -)Couldn't classify 5106, 5130
Sorry, prediction GeneMark_model.108107_t fails validation.
(ATG)	 GT	4205-4219	GT	CTG
(CGT)	 AG	4285-4453	GT	CGG
(TGG)	 AG	4687-4795	GT	GGG
(TGA)	 AG	4895-5004	GT	CGG
(ACC)	 AG	5106-5130	GT	AGG
-recovered GeneMark_model.108107_t, initial, 4205, 4219
-recovered GeneMark_model.108107_t, internal, 4285, 4453
-recovered GeneMark_model.108107_t, internal, 4687, 4795
-recovered GeneMark_model.108107_t, internal, 4895, 5004
-recovered GeneMark_model.108107_t, internal, 5106, 5130
Couldn't classify 38, 178
Couldn't classify 2210, 2280
Sorry, prediction pasa_asmbl_49427.p1 fails validation.
(CTG)	 TG	38-178	GT	AGG
(GCT)	 AG	424-642	GT	AGG
(CTG)	 AG	885-999	GT	CAG
(AGT)	 AG	1225-1385	GT	AGG
(CCA)	 AG	1834-2035	GT	AGG
(CCG)	 AG	2210-2280	TC	TGT
-recovered pasa_asmbl_49427.p1, internal, 424, 642
-recovered pasa_asmbl_49427.p1, internal, 885, 999
-recovered pasa_asmbl_49427.p1, internal, 1225, 1385
-recovered pasa_asmbl_49427.p1, internal, 1834, 2035
Couldn't classify 32, 178
Sorry, prediction GeneMark_model.108111_t fails validation.
(GTG)	 AG	32-178	GT	AGG
(GCT)	 AG	424-642	GT	AGG
(TCG)	 AG	894-999	GT	CAG
(AGT)	 AG	1225-1385	GT	AGG
(CCA)	 AG	1834-2035	GT	AGG
(GGG)	 AG	2071-2130	GT	TGG
(CCG)	 AG	2210-2394	GT	GGG
(GGA)	 AG	2528-2863	AG	GAA
-recovered GeneMark_model.108111_t, terminal, 2528, 2863
-recovered GeneMark_model.108111_t, internal, 32, 178
-recovered GeneMark_model.108111_t, internal, 424, 642
-recovered GeneMark_model.108111_t, internal, 894, 999
-recovered GeneMark_model.108111_t, internal, 1225, 1385
-recovered GeneMark_model.108111_t, internal, 1834, 2035
-recovered GeneMark_model.108111_t, internal, 2071, 2130
-recovered GeneMark_model.108111_t, internal, 2210, 2394
Couldn't classify 89, 178
Sorry, prediction GlimmerHMM_glimmerT_62075-T1 fails validation.
(CAC)	 AG	89-178	GT	AGG
(GCT)	 AG	424-642	GT	AGG
(CTG)	 AG	885-999	GT	CAG
(AGT)	 AG	1225-1385	GT	AGG
(CCA)	 AG	1834-2035	GT	AGG
(CCG)	 AG	2210-2394	GT	GGG
(GGA)	 AG	2528-2789	GT	AGG
(GTA)	 AG	3112-3278	GT	CGG
(CGT)	 AG	4285-4453	GT	CGG
(TGG)	 AG	4687-4795	GT	GGG
(TGA)	 AG	4895-5105	AC	AGA
-recovered GlimmerHMM_glimmerT_62075-T1, terminal, 4895, 5105
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 89, 178
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 424, 642
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 885, 999
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 1225, 1385
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 1834, 2035
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 2210, 2394
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 2528, 2789
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 3112, 3278
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 4285, 4453
-recovered GlimmerHMM_glimmerT_62075-T1, internal, 4687, 4795
Couldn't classify 32, 178
Couldn't classify 4895, 5004
Sorry, prediction snap_scaffold_641-snap.1-T1 fails validation.
(GTG)	 AG	32-178	GT	AGG
(GCT)	 AG	424-642	GT	AGG
(CTG)	 AG	885-999	GT	CAG
(AGT)	 AG	1225-1385	GT	AGG
(CCA)	 AG	1834-2035	GT	AGG
(CCG)	 AG	2210-2394	GT	GGG
(GGA)	 AG	2528-2789	GT	AGG
(GTA)	 AG	3112-3278	GT	CGG
(CGT)	 AG	4285-4453	GT	CGG
(TGG)	 AG	4687-4795	GT	GGG
(TGA)	 AG	4895-5004	GT	CGG
-recovered snap_scaffold_641-snap.1-T1, internal, 32, 178
-recovered snap_scaffold_641-snap.1-T1, internal, 424, 642
-recovered snap_scaffold_641-snap.1-T1, internal, 885, 999
-recovered snap_scaffold_641-snap.1-T1, internal, 1225, 1385
-recovered snap_scaffold_641-snap.1-T1, internal, 1834, 2035
-recovered snap_scaffold_641-snap.1-T1, internal, 2210, 2394
-recovered snap_scaffold_641-snap.1-T1, internal, 2528, 2789
-recovered snap_scaffold_641-snap.1-T1, internal, 3112, 3278
-recovered snap_scaffold_641-snap.1-T1, internal, 4285, 4453
-recovered snap_scaffold_641-snap.1-T1, internal, 4687, 4795
-recovered snap_scaffold_641-snap.1-T1, internal, 4895, 5004
Couldn't classify 4895, 5004
Sorry, prediction Augustus_model.g41263.t1 fails validation.
(ATG)	 CA	299-304	GT	AGG
(GCT)	 AG	424-642	GT	AGG
(CTG)	 AG	885-999	GT	CAG
(AGT)	 AG	1225-1385	GT	AGG
(CCA)	 AG	1834-2035	GT	AGG
(CCG)	 AG	2210-2394	GT	GGG
(GGA)	 AG	2528-2789	GT	AGG
(GTA)	 AG	3112-3278	GT	CGG
(CGT)	 AG	4285-4453	GT	CGG
(TGG)	 AG	4687-4795	GT	GGG
(TGA)	 AG	4895-5004	GT	CGG
-recovered Augustus_model.g41263.t1, initial, 299, 304
-recovered Augustus_model.g41263.t1, internal, 424, 642
-recovered Augustus_model.g41263.t1, internal, 885, 999
-recovered Augustus_model.g41263.t1, internal, 1225, 1385
-recovered Augustus_model.g41263.t1, internal, 1834, 2035
-recovered Augustus_model.g41263.t1, internal, 2210, 2394
-recovered Augustus_model.g41263.t1, internal, 2528, 2789
-recovered Augustus_model.g41263.t1, internal, 3112, 3278
-recovered Augustus_model.g41263.t1, internal, 4285, 4453
-recovered Augustus_model.g41263.t1, internal, 4687, 4795
-recovered Augustus_model.g41263.t1, internal, 4895, 5004
Couldn't classify 3117, 3278
Couldn't classify 4895, 4997
Sorry, prediction pasa_asmbl_49426.p1 fails validation.
(CTT)	 AA	3117-3278	GT	CGG
(CGT)	 AG	4285-4453	GT	CGG
(TGG)	 AG	4687-4795	GT	GGG
(TGA)	 AG	4895-4997	GT	CCG
-recovered pasa_asmbl_49426.p1, internal, 4285, 4453
-recovered pasa_asmbl_49426.p1, internal, 4687, 4795
-recovered pasa_asmbl_49426.p1, internal, 4895, 4997

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

-building trellis in range 1 - 5225
-exon list size: 48


building trellis

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

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support