-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_16166816-16347257

-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_10-snap.3306-T1
Valid prediction for GeneMark_model.45849_t
Valid prediction for GeneMark_model.45883_t
Valid prediction for snap_scaffold_10-snap.3326-T1
Valid prediction for GlimmerHMM_glimmerT_26625-T1
Valid prediction for GlimmerHMM_glimmerT_26620-T1
Valid prediction for GlimmerHMM_glimmerT_26640-T1
Valid prediction for GeneMark_model.45872_t
Valid prediction for GeneMark_model.45846_t
Valid prediction for GeneMark_model.45865_t
Valid prediction for snap_scaffold_10-snap.3313-T1
Valid prediction for GeneMark_model.45867_t
Couldn't classify 49746, 49901
Sorry, prediction pasa_asmbl_4980.p1 fails validation.
(ATG)	 TC	49310-49468	GT	AGG
(GAT)	 AG	49746-49901	AG	TGA
-recovered pasa_asmbl_4980.p1, initial, 49310, 49468
Valid prediction for snap_scaffold_10-snap.3308-T1
Valid prediction for GlimmerHMM_glimmerT_26626-T1
Valid prediction for CodingQuarry_transcript_5653-T1
Valid prediction for GlimmerHMM_glimmerT_26639-T1
Valid prediction for GeneMark_model.45851_t
Valid prediction for snap_scaffold_10-snap.3298-T1
Valid prediction for GeneMark_model.45886_t
Valid prediction for snap_scaffold_10-snap.3296-T1
Valid prediction for GeneMark_model.45880_t
Valid prediction for snap_scaffold_10-snap.3309-T1
Valid prediction for snap_scaffold_10-snap.3304-T1
Valid prediction for GeneMark_model.45893_t
Valid prediction for snap_scaffold_10-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_26632-T1
Valid prediction for snap_scaffold_10-snap.3324-T1
Valid prediction for snap_scaffold_10-snap.3295-T1
Valid prediction for snap_scaffold_10-snap.3315-T1
Couldn't classify 85940, 86219
Sorry, prediction pasa_asmbl_4984.p1 fails validation.
(GTC)	 AT	85940-86219	GT	CAG
(AGA)	 AG	87075-87139	GT	AGG
(GGA)	 AG	87301-87342	GT	AGG
(GTG)	 AG	87450-87503	GC	AGG
(ATT)	 AG	88106-88225	GT	AGG
(ACG)	 AG	89177-89263	GT	AGG
(GTG)	 AG	89872-89998	GT	CAG
(GTA)	 AG	90775-90902	GT	AGG
(GAC)	 AG	91662-91747	GT	TGG
(CAA)	 AG	92635-92704	GT	CGG
(GCT)	 AG	93118-93157	GT	AGG
(TGG)	 AG	93292-93320	TT	GAT
-recovered pasa_asmbl_4984.p1, terminal, 93292, 93320
-recovered pasa_asmbl_4984.p1, internal, 87075, 87139
-recovered pasa_asmbl_4984.p1, internal, 87301, 87342
-recovered pasa_asmbl_4984.p1, internal, 87450, 87503
-recovered pasa_asmbl_4984.p1, internal, 88106, 88225
-recovered pasa_asmbl_4984.p1, internal, 89177, 89263
-recovered pasa_asmbl_4984.p1, internal, 89872, 89998
-recovered pasa_asmbl_4984.p1, internal, 90775, 90902
-recovered pasa_asmbl_4984.p1, internal, 91662, 91747
-recovered pasa_asmbl_4984.p1, internal, 92635, 92704
-recovered pasa_asmbl_4984.p1, internal, 93118, 93157
Valid prediction for GeneMark_model.45840_t
Valid prediction for GeneMark_model.45839_t
Valid prediction for GeneMark_model.45862_t
Valid prediction for snap_scaffold_10-snap.3321-T1
Valid prediction for GeneMark_model.45874_t
Valid prediction for Augustus_model.g17850.t1
Valid prediction for GeneMark_model.45853_t
Valid prediction for GeneMark_model.45895_t
Valid prediction for GeneMark_model.45842_t
Valid prediction for GeneMark_model.45852_t
Valid prediction for GeneMark_model.45891_t
Valid prediction for snap_scaffold_10-snap.3302-T1
Valid prediction for GeneMark_model.45843_t
Couldn't classify 91229, 91447
Sorry, prediction pasa_asmbl_4985.p1 fails validation.
(GTG)	 GT	91229-91447	GT	AGG
(GAC)	 AG	91662-91747	GT	TGG
(CAA)	 AG	92635-92704	GT	CGG
(GCT)	 AG	93118-93157	GT	AGG
(TGG)	 AG	93292-93320	TT	GAT
-recovered pasa_asmbl_4985.p1, terminal, 93292, 93320
-recovered pasa_asmbl_4985.p1, internal, 91662, 91747
-recovered pasa_asmbl_4985.p1, internal, 92635, 92704
-recovered pasa_asmbl_4985.p1, internal, 93118, 93157
Valid prediction for snap_scaffold_10-snap.3316-T1
Valid prediction for GeneMark_model.45847_t
Valid prediction for Augustus_model.g17853.t1
Valid prediction for snap_scaffold_10-snap.3322-T1
Valid prediction for GeneMark_model.45860_t
Valid prediction for GeneMark_model.45857_t
Valid prediction for snap_scaffold_10-snap.3331-T1
Valid prediction for GeneMark_model.45889_t
Valid prediction for snap_scaffold_10-snap.3294-T1
Valid prediction for GlimmerHMM_glimmerT_26634-T1
Valid prediction for snap_scaffold_10-snap.3297-T1
Valid prediction for Augustus_model.g17847.t1
Valid prediction for GeneMark_model.45859_t
Valid prediction for snap_scaffold_10-snap.3300-T1
Valid prediction for GeneMark_model.45855_t
Valid prediction for GeneMark_model.45869_t
Valid prediction for GeneMark_model.45844_t
Valid prediction for snap_scaffold_10-snap.3318-T1
Valid prediction for Augustus_model.g17856.t1
Valid prediction for GeneMark_model.45885_t
Valid prediction for GlimmerHMM_glimmerT_26623-T1
Valid prediction for snap_scaffold_10-snap.3301-T1
Valid prediction for snap_scaffold_10-snap.3325-T1
Valid prediction for CodingQuarry_transcript_5652-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_10-snap.3314-T1
Valid prediction for GeneMark_model.45856_t
Valid prediction for snap_scaffold_10-snap.3305-T1
Valid prediction for GlimmerHMM_glimmerT_26633-T1
Valid prediction for GeneMark_model.45864_t
Valid prediction for GeneMark_model.45866_t
Valid prediction for snap_scaffold_10-snap.3310-T1
Valid prediction for GeneMark_model.45845_t
Valid prediction for GeneMark_model.45878_t
Valid prediction for GlimmerHMM_glimmerT_26629-T1
Valid prediction for GlimmerHMM_glimmerT_26641-T1
Valid prediction for GeneMark_model.45877_t
Valid prediction for GlimmerHMM_glimmerT_26635-T1
Valid prediction for GlimmerHMM_glimmerT_26636-T1
Valid prediction for GlimmerHMM_glimmerT_26621-T1
Valid prediction for GeneMark_model.45892_t
Couldn't classify 74840, 76058
Couldn't classify 78349, 78522
Sorry, prediction pasa_asmbl_3898.p1 fails validation.
(CAA)	 AA	74840-76058	GT	TGG
(ATC)	 AG	76665-76755	GT	AGG
(GTC)	 AG	77724-77817	GT	GGG
(GTG)	 AG	78349-78522	GC	GAG
-recovered pasa_asmbl_3898.p1, internal, 76665, 76755
-recovered pasa_asmbl_3898.p1, internal, 77724, 77817
-recovered pasa_asmbl_3898.p1, internal, 78349, 78522
Valid prediction for GlimmerHMM_glimmerT_26628-T1
Couldn't classify 72992, 74041
Sorry, prediction pasa_asmbl_3899.p1 fails validation.
(GGG)	 AG	72992-74041	TT	GCT
Valid prediction for pasa_asmbl_4124.p1
Valid prediction for snap_scaffold_10-snap.3307-T1
Valid prediction for GlimmerHMM_glimmerT_26627-T1
Valid prediction for GeneMark_model.45876_t
Valid prediction for GeneMark_model.45894_t
Valid prediction for snap_scaffold_10-snap.3317-T1
Valid prediction for GeneMark_model.45887_t
Valid prediction for GeneMark_model.45890_t
Valid prediction for GeneMark_model.45858_t
Valid prediction for Augustus_model.g17851.t1
Valid prediction for snap_scaffold_10-snap.3299-T1
Valid prediction for GeneMark_model.45868_t
Valid prediction for snap_scaffold_10-snap.3323-T1
Valid prediction for GeneMark_model.45873_t
Valid prediction for snap_scaffold_10-snap.3327-T1
Valid prediction for GeneMark_model.45870_t
Valid prediction for Augustus_model.g17854.t1
Valid prediction for GeneMark_model.45884_t
Valid prediction for GeneMark_model.45888_t
Valid prediction for snap_scaffold_10-snap.3329-T1
Valid prediction for GeneMark_model.45879_t
Valid prediction for Augustus_model.g17855.t1
Valid prediction for GeneMark_model.45863_t
Valid prediction for GeneMark_model.45871_t
Valid prediction for GlimmerHMM_glimmerT_26624-T1
Valid prediction for snap_scaffold_10-snap.3312-T1
Valid prediction for GlimmerHMM_glimmerT_26630-T1
Valid prediction for GeneMark_model.45882_t
Valid prediction for GeneMark_model.45875_t
Valid prediction for snap_scaffold_10-snap.3320-T1
Valid prediction for GeneMark_model.45848_t
Valid prediction for GlimmerHMM_glimmerT_26622-T1
Valid prediction for Augustus_model.g17849.t1
Valid prediction for snap_scaffold_10-snap.3293-T1
Valid prediction for GeneMark_model.45881_t
Valid prediction for snap_scaffold_10-snap.3328-T1
Valid prediction for GlimmerHMM_glimmerT_26638-T1
Valid prediction for GeneMark_model.45861_t
Valid prediction for snap_scaffold_10-snap.3311-T1
Valid prediction for GeneMark_model.45850_t
Valid prediction for GeneMark_model.45841_t
Valid prediction for snap_scaffold_10-snap.3303-T1
Valid prediction for GeneMark_model.45838_t
Valid prediction for Augustus_model.g17848.t1
Valid prediction for snap_scaffold_10-snap.3332-T1
Valid prediction for GlimmerHMM_glimmerT_26637-T1
Valid prediction for Augustus_model.g17852.t1
Valid prediction for GeneMark_model.45854_t
Valid prediction for GlimmerHMM_glimmerT_26631-T1
Valid prediction for snap_scaffold_10-snap.3319-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30523, rend_intergenic: 5353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34367, rend_intergenic: 31040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48248, rend_intergenic: 34785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53854, rend_intergenic: 51041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58207, rend_intergenic: 55401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66997, rend_intergenic: 60879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73010, rend_intergenic: 67609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76212, rend_intergenic: 73104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92802, rend_intergenic: 89850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103924, rend_intergenic: 99393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105108, rend_intergenic: 104377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119653, rend_intergenic: 108073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152572, rend_intergenic: 146633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161195, rend_intergenic: 153911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162529, rend_intergenic: 161750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173191, rend_intergenic: 166670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180442
-exon list size: 677


building trellis

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91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 30523, rend_intergenic: 5353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34367, rend_intergenic: 31040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48248, rend_intergenic: 34785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53854, rend_intergenic: 51041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58207, rend_intergenic: 55401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66997, rend_intergenic: 60879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73010, rend_intergenic: 67609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76212, rend_intergenic: 73104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92802, rend_intergenic: 89850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103924, rend_intergenic: 99393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105108, rend_intergenic: 104377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119653, rend_intergenic: 108073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152572, rend_intergenic: 146633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161195, rend_intergenic: 153911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162529, rend_intergenic: 161750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173191, rend_intergenic: 166670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support