-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_5104517-5245742

-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.801_t
Couldn't classify 35289, 35550
Sorry, prediction pasa_asmbl_1699.p2 fails validation.
(GTG)	 GT	35289-35550	GT	GGG
(GGT)	 AG	35817-36010	CC	GAC
-recovered pasa_asmbl_1699.p2, terminal, 35817, 36010
Valid prediction for GlimmerHMM_glimmerT_636-T1
Valid prediction for GeneMark_model.790_t
Valid prediction for snap_scaffold_1-snap.786-T1
Valid prediction for Augustus_model.g478.t1
Valid prediction for GeneMark_model.787_t
Valid prediction for GlimmerHMM_glimmerT_635-T1
Valid prediction for GeneMark_model.785_t
Valid prediction for GlimmerHMM_glimmerT_629-T1
Valid prediction for GeneMark_model.796_t
Valid prediction for snap_scaffold_1-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_626-T1
Couldn't classify 105721, 105855
Sorry, prediction pasa_asmbl_1710.p1 fails validation.
(ATG)	 CT	103614-103664	GT	TAG
(CGC)	 AG	103790-103907	GT	TGG
(GGG)	 AG	104073-104157	GT	AGG
(GAA)	 AG	104256-104432	GT	GAG
(TTA)	 AG	104623-104669	GT	CAG
(ACA)	 AG	104777-104895	GT	TGG
(TCT)	 AG	105000-105131	GT	AGG
(ATC)	 AG	105721-105855	GT	AGG
-recovered pasa_asmbl_1710.p1, initial, 103614, 103664
-recovered pasa_asmbl_1710.p1, internal, 103790, 103907
-recovered pasa_asmbl_1710.p1, internal, 104073, 104157
-recovered pasa_asmbl_1710.p1, internal, 104256, 104432
-recovered pasa_asmbl_1710.p1, internal, 104623, 104669
-recovered pasa_asmbl_1710.p1, internal, 104777, 104895
-recovered pasa_asmbl_1710.p1, internal, 105000, 105131
-recovered pasa_asmbl_1710.p1, internal, 105721, 105855
Valid prediction for Augustus_model.g480.t1
Valid prediction for GlimmerHMM_glimmerT_628-T1
Valid prediction for GeneMark_model.798_t
Valid prediction for GeneMark_model.783_t
Valid prediction for GeneMark_model.797_t
Valid prediction for HiQ_model.g486.t1
Valid prediction for GlimmerHMM_glimmerT_621-T1
Valid prediction for snap_scaffold_1-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_639-T1
Valid prediction for Augustus_model.g476.t1
Valid prediction for GeneMark_model.809_t
Valid prediction for snap_scaffold_1-snap.798-T1
Valid prediction for Augustus_model.g473.t1
Valid prediction for GlimmerHMM_glimmerT_638-T1
Valid prediction for GlimmerHMM_glimmerT_622-T1
Valid prediction for snap_scaffold_1-snap.817-T1
Couldn't classify 19624, 19706
Couldn't classify 22953, 23068
Sorry, prediction pasa_asmbl_1693.p1 fails validation.
(GAG)	 CC	19624-19706	GT	AGG
(TAA)	 AG	20142-20320	GT	GGG
(GTA)	 AG	22953-23068	AC	CCA
-recovered pasa_asmbl_1693.p1, internal, 20142, 20320
Valid prediction for GeneMark_model.780_t
Valid prediction for GlimmerHMM_glimmerT_624-T1
Valid prediction for GeneMark_model.792_t
Valid prediction for Augustus_model.g489.t1
Valid prediction for snap_scaffold_1-snap.788-T1
Valid prediction for snap_scaffold_1-snap.807-T1
Valid prediction for GeneMark_model.794_t
Valid prediction for pasa_asmbl_1701.p1
Valid prediction for snap_scaffold_1-snap.793-T1
Valid prediction for snap_scaffold_1-snap.791-T1
Valid prediction for CodingQuarry_transcript_2598-T1
Valid prediction for HiQ_model.g481.t1
Valid prediction for snap_scaffold_1-snap.812-T1
Valid prediction for snap_scaffold_1-snap.787-T1
Couldn't classify 26006, 26208
Couldn't classify 27682, 27765
Sorry, prediction pasa_asmbl_1695.p1 fails validation.
(GCC)	 CA	26006-26208	GT	AGG
(GTT)	 AG	27066-27233	GT	CGG
(GGA)	 AG	27351-27465	GT	AGG
(GTT)	 AG	27682-27765	GT	TGG
-recovered pasa_asmbl_1695.p1, internal, 27066, 27233
-recovered pasa_asmbl_1695.p1, internal, 27351, 27465
-recovered pasa_asmbl_1695.p1, internal, 27682, 27765
Valid prediction for snap_scaffold_1-snap.810-T1
Valid prediction for GlimmerHMM_glimmerT_631-T1
Couldn't classify 105721, 105855
Sorry, prediction pasa_asmbl_1707.p1 fails validation.
(ATG)	 CC	100089-100292	GT	TGG
(GTG)	 AG	100403-100515	GT	AGG
(CCG)	 AG	100691-100793	GT	TTG
(GTG)	 AG	100877-101034	GT	CTG
(CTT)	 AG	101290-101382	GT	AGG
(CTC)	 AG	101967-102120	GT	AGG
(CTA)	 AG	102729-102842	GT	AGG
(GAT)	 AG	103336-103360	GT	TGG
(AGA)	 AG	103561-103664	GT	TAG
(CGC)	 AG	103790-103907	GT	TGG
(GGG)	 AG	104073-104157	GT	AGG
(GAA)	 AG	104256-104432	GT	GAG
(TTA)	 AG	104623-104669	GT	CAG
(ACA)	 AG	104777-104895	GT	TGG
(TCT)	 AG	105000-105131	GT	AGG
(ATC)	 AG	105721-105855	GT	AGG
-recovered pasa_asmbl_1707.p1, initial, 100089, 100292
-recovered pasa_asmbl_1707.p1, internal, 100403, 100515
-recovered pasa_asmbl_1707.p1, internal, 100691, 100793
-recovered pasa_asmbl_1707.p1, internal, 100877, 101034
-recovered pasa_asmbl_1707.p1, internal, 101290, 101382
-recovered pasa_asmbl_1707.p1, internal, 101967, 102120
-recovered pasa_asmbl_1707.p1, internal, 102729, 102842
-recovered pasa_asmbl_1707.p1, internal, 103336, 103360
-recovered pasa_asmbl_1707.p1, internal, 103561, 103664
-recovered pasa_asmbl_1707.p1, internal, 103790, 103907
-recovered pasa_asmbl_1707.p1, internal, 104073, 104157
-recovered pasa_asmbl_1707.p1, internal, 104256, 104432
-recovered pasa_asmbl_1707.p1, internal, 104623, 104669
-recovered pasa_asmbl_1707.p1, internal, 104777, 104895
-recovered pasa_asmbl_1707.p1, internal, 105000, 105131
-recovered pasa_asmbl_1707.p1, internal, 105721, 105855
Valid prediction for snap_scaffold_1-snap.792-T1
Valid prediction for GeneMark_model.807_t
Valid prediction for Augustus_model.g488.t1
Valid prediction for snap_scaffold_1-snap.795-T1
Valid prediction for Augustus_model.g479.t1
Valid prediction for Augustus_model.g474.t1
Valid prediction for snap_scaffold_1-snap.800-T1
Valid prediction for snap_scaffold_1-snap.801-T1
Couldn't classify 29519, 29536
Couldn't classify 29928, 30233
Sorry, prediction pasa_asmbl_2691.p1 fails validation.
(CTG)	 TG	29519-29536	GT	AGG
(GTG)	 AG	29928-30233	AA	TGA
Valid prediction for GeneMark_model.803_t
Valid prediction for Augustus_model.g472.t1
Valid prediction for snap_scaffold_1-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_630-T1
Valid prediction for GeneMark_model.782_t
Valid prediction for CodingQuarry_transcript_2601-T1
Valid prediction for CodingQuarry_transcript_2602-T1
Couldn't classify 31130, 31201
Sorry, prediction pasa_asmbl_1697.p1 fails validation.
(GGC)	 GA	31130-31201	GT	AGG
(CAG)	 AG	31429-31584	GT	AGG
(CTG)	 AG	33123-33332	GT	AGG
(GAA)	 AG	33507-33665	GT	AGG
(ATC)	 AG	33767-33950	GT	AGG
(ATG)	 AG	34173-34295	GT	AGG
(CCG)	 AG	34738-34874	GT	GGG
(AGT)	 AG	34990-35095	GT	CGG
(AGA)	 AG	35314-35550	GT	GGG
(GGT)	 AG	35817-36010	CC	GAC
add_exon() Sorry, pasa_asmbl_1697.p1 34173-34295-initial-1 is invalid.
-recovered pasa_asmbl_1697.p1, initial, 34173, 34295
-recovered pasa_asmbl_1697.p1, terminal, 35817, 36010
-recovered pasa_asmbl_1697.p1, internal, 31429, 31584
-recovered pasa_asmbl_1697.p1, internal, 33123, 33332
-recovered pasa_asmbl_1697.p1, internal, 33507, 33665
-recovered pasa_asmbl_1697.p1, internal, 33767, 33950
-recovered pasa_asmbl_1697.p1, internal, 34173, 34295
-recovered pasa_asmbl_1697.p1, internal, 34738, 34874
-recovered pasa_asmbl_1697.p1, internal, 34990, 35095
-recovered pasa_asmbl_1697.p1, internal, 35314, 35550

-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_633-T1
Valid prediction for snap_scaffold_1-snap.816-T1
Valid prediction for HiQ_model.g487.t1
Valid prediction for pasa_asmbl_243.p1
Valid prediction for snap_scaffold_1-snap.813-T1
Valid prediction for CodingQuarry_transcript_2599-T1
Valid prediction for snap_scaffold_1-snap.804-T1
Valid prediction for Augustus_model.g471.t1
Valid prediction for GeneMark_model.781_t
Valid prediction for snap_scaffold_1-snap.796-T1
Valid prediction for snap_scaffold_1-snap.814-T1
Valid prediction for GlimmerHMM_glimmerT_637-T1
Valid prediction for snap_scaffold_1-snap.808-T1
Valid prediction for CodingQuarry_transcript_2603-T1
Valid prediction for GlimmerHMM_glimmerT_625-T1
Valid prediction for GeneMark_model.786_t
Valid prediction for snap_scaffold_1-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_641-T1
Valid prediction for snap_scaffold_1-snap.802-T1
Valid prediction for GeneMark_model.788_t
Valid prediction for GeneMark_model.804_t
Valid prediction for GlimmerHMM_glimmerT_640-T1
Valid prediction for snap_scaffold_1-snap.811-T1
Valid prediction for snap_scaffold_1-snap.790-T1
Valid prediction for GeneMark_model.784_t
Valid prediction for snap_scaffold_1-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_623-T1
Valid prediction for GlimmerHMM_glimmerT_620-T1
Valid prediction for GeneMark_model.793_t
Valid prediction for Augustus_model.g477.t1
Valid prediction for Augustus_model.g485.t1
Valid prediction for GlimmerHMM_glimmerT_632-T1
Valid prediction for HiQ_model.g483.t1
Valid prediction for Augustus_model.g484.t1
Valid prediction for GeneMark_model.779_t
Couldn't classify 60004, 60033
Sorry, prediction pasa_asmbl_240.p1 fails validation.
(GTA)	 TG	60004-60033	GT	CGG
(GCT)	 AG	60143-60176	GT	AGG
(CGG)	 AG	60320-60494	GT	AGG
(GTT)	 AG	60727-60915	GT	GGG
(TGA)	 AG	61145-61547	TC	GAT
add_exon() Sorry, pasa_asmbl_240.p1 60320-60494-terminal-3 is invalid.
-recovered pasa_asmbl_240.p1, terminal, 60320, 60494
-recovered pasa_asmbl_240.p1, terminal, 61145, 61547
-recovered pasa_asmbl_240.p1, internal, 60143, 60176
-recovered pasa_asmbl_240.p1, internal, 60320, 60494
-recovered pasa_asmbl_240.p1, internal, 60727, 60915
Valid prediction for GeneMark_model.791_t
Valid prediction for pasa_asmbl_255.p1
Valid prediction for GeneMark_model.802_t
Valid prediction for GeneMark_model.789_t
Valid prediction for Augustus_model.g491.t1
Valid prediction for pasa_asmbl_250.p1
Valid prediction for Augustus_model.g475.t1
Valid prediction for GlimmerHMM_glimmerT_642-T1
Valid prediction for snap_scaffold_1-snap.805-T1
Valid prediction for CodingQuarry_transcript_2600-T1
Valid prediction for pasa_asmbl_251.p1
Valid prediction for HiQ_model.g490.t1
Valid prediction for snap_scaffold_1-snap.803-T1
Valid prediction for snap_scaffold_1-snap.794-T1
Valid prediction for GlimmerHMM_glimmerT_634-T1
Valid prediction for GeneMark_model.800_t
Valid prediction for GeneMark_model.795_t
Valid prediction for snap_scaffold_1-snap.806-T1
Valid prediction for GeneMark_model.806_t
Valid prediction for GeneMark_model.805_t
Couldn't classify 44886, 44937
Sorry, prediction pasa_asmbl_245.p2 fails validation.
(CAG)	 CG	44886-44937	GT	AGG
(GTT)	 AG	46293-46418	GT	AGG
(ATC)	 AG	46940-47005	GT	CGG
(CTT)	 AG	47401-47599	GT	AGG
(GTG)	 AG	47968-48085	TC	AAT
-recovered pasa_asmbl_245.p2, terminal, 47968, 48085
-recovered pasa_asmbl_245.p2, internal, 46293, 46418
-recovered pasa_asmbl_245.p2, internal, 46940, 47005
-recovered pasa_asmbl_245.p2, internal, 47401, 47599
Valid prediction for GeneMark_model.808_t
Valid prediction for GlimmerHMM_glimmerT_627-T1
Valid prediction for Augustus_model.g482.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36010, rend_intergenic: 18066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50803, rend_intergenic: 47461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 141226
-exon list size: 464


building trellis

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22.7    
23.0    
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29.8    
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34.5    
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35.6    
35.8    
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41.6    
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99.1    
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99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 36010, rend_intergenic: 18066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50803, rend_intergenic: 47461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support