-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_10266778-10475662

-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_30602-T1
Valid prediction for GeneMark_model.52840_t
Valid prediction for snap_scaffold_12-snap.1963-T1
Valid prediction for GeneMark_model.52853_t
Valid prediction for GlimmerHMM_glimmerT_30584-T1
Valid prediction for HiQ_model.g20400.t1
Couldn't classify 92195, 92270
Couldn't classify 93108, 93299
Sorry, prediction pasa_asmbl_8885.p1 fails validation.
(GAG)	 CT	92195-92270	GT	AGG
(ACT)	 AG	92679-92887	GT	AGG
(TTG)	 AG	93108-93299	GA	CGG
-recovered pasa_asmbl_8885.p1, internal, 92679, 92887
Valid prediction for GlimmerHMM_glimmerT_30590-T1
Couldn't classify 90659, 90862
Couldn't classify 91809, 91861
Sorry, prediction pasa_asmbl_9191.p2 fails validation.
(GAG)	 CT	90659-90862	GT	AAG
(AAG)	 AG	91222-91345	GT	AGG
(GTA)	 AG	91809-91861	CA	GTC
-recovered pasa_asmbl_9191.p2, internal, 91222, 91345
Valid prediction for GeneMark_model.52839_t
Valid prediction for pasa_asmbl_8887.p1
Valid prediction for GlimmerHMM_glimmerT_30599-T1
Valid prediction for snap_scaffold_12-snap.1985-T1
Valid prediction for Augustus_model.g20395.t1
Valid prediction for GeneMark_model.52859_t
Valid prediction for GlimmerHMM_glimmerT_30612-T1
Valid prediction for GlimmerHMM_glimmerT_30609-T1
Valid prediction for GeneMark_model.52868_t
Valid prediction for GlimmerHMM_glimmerT_30592-T1
Valid prediction for snap_scaffold_12-snap.1976-T1
Valid prediction for Augustus_model.g20396.t1
Valid prediction for CodingQuarry_transcript_10343-T1
Valid prediction for snap_scaffold_12-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_30611-T1
Valid prediction for snap_scaffold_12-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_30596-T1
Valid prediction for snap_scaffold_12-snap.1977-T1
Valid prediction for Augustus_model.g20407.t1
Valid prediction for GeneMark_model.52861_t
Valid prediction for snap_scaffold_12-snap.1995-T1
Valid prediction for GeneMark_model.52850_t
Valid prediction for GlimmerHMM_glimmerT_30591-T1
Valid prediction for GeneMark_model.52843_t
Couldn't classify 66107, 66138
Sorry, prediction pasa_asmbl_8884.p1 fails validation.
(TGC)	 CC	66107-66138	GT	AGG
(GTG)	 AG	67462-67721	GT	AAG
(TAA)	 AG	67826-68694	GG	GAG
-recovered pasa_asmbl_8884.p1, terminal, 67826, 68694
-recovered pasa_asmbl_8884.p1, internal, 67462, 67721
Valid prediction for snap_scaffold_12-snap.1982-T1
Valid prediction for snap_scaffold_12-snap.1992-T1
Valid prediction for GeneMark_model.52854_t
Valid prediction for snap_scaffold_12-snap.1972-T1
Valid prediction for GeneMark_model.52865_t
Valid prediction for snap_scaffold_12-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_30595-T1
Couldn't classify 63704, 64075
Sorry, prediction pasa_asmbl_8883.p1 fails validation.
(ATG)	 AA	63704-64075	TA	GGT
Valid prediction for GeneMark_model.52845_t
Valid prediction for Augustus_model.g20403.t1
Valid prediction for snap_scaffold_12-snap.1974-T1
Valid prediction for snap_scaffold_12-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_30594-T1
Valid prediction for GlimmerHMM_glimmerT_30608-T1
Valid prediction for GeneMark_model.52860_t
Valid prediction for GlimmerHMM_glimmerT_30610-T1
Valid prediction for snap_scaffold_12-snap.1965-T1
Valid prediction for Augustus_model.g20398.t1
Valid prediction for GeneMark_model.52851_t
Valid prediction for GeneMark_model.52869_t
Valid prediction for GeneMark_model.52841_t
Valid prediction for GlimmerHMM_glimmerT_30586-T1
Valid prediction for snap_scaffold_12-snap.1990-T1
Valid prediction for snap_scaffold_12-snap.1966-T1
Valid prediction for GeneMark_model.52866_t
Valid prediction for GlimmerHMM_glimmerT_30603-T1
Valid prediction for snap_scaffold_12-snap.1970-T1
Valid prediction for GeneMark_model.52848_t
Valid prediction for GeneMark_model.52856_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: -)Valid prediction for Augustus_model.g20391.t1
Couldn't classify 96124, 96318
Sorry, prediction pasa_asmbl_7878.p1 fails validation.
(GAT)	 TG	96124-96318	GT	GGG
(TTC)	 AG	97438-97626	GT	TGG
(TAT)	 AG	97731-97805	GT	AGG
(ATC)	 AG	97886-97981	GT	CTG
(TTG)	 AG	99252-99407	GT	AGG
(GGC)	 AG	99536-99619	GT	AGG
(CTC)	 AG	99738-99806	CT	AGC
-recovered pasa_asmbl_7878.p1, terminal, 99738, 99806
-recovered pasa_asmbl_7878.p1, internal, 97438, 97626
-recovered pasa_asmbl_7878.p1, internal, 97731, 97805
-recovered pasa_asmbl_7878.p1, internal, 97886, 97981
-recovered pasa_asmbl_7878.p1, internal, 99252, 99407
-recovered pasa_asmbl_7878.p1, internal, 99536, 99619
Valid prediction for snap_scaffold_12-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_30600-T1
Valid prediction for Augustus_model.g20402.t1
Valid prediction for snap_scaffold_12-snap.1980-T1
Valid prediction for GlimmerHMM_glimmerT_30583-T1
Valid prediction for snap_scaffold_12-snap.1964-T1
Couldn't classify 47837, 48037
Couldn't classify 48621, 48692
Sorry, prediction pasa_asmbl_8321.p1 fails validation.
(CTC)	 GG	47837-48037	GT	AGG
(GAG)	 AG	48129-48218	GT	ACG
(GTG)	 AG	48621-48692	GA	CCG
-recovered pasa_asmbl_8321.p1, internal, 48129, 48218
Couldn't classify 83818, 83942
Sorry, prediction pasa_asmbl_7880.p1 fails validation.
(GGA)	 AG	83818-83942	GT	CGG
(GAA)	 AG	84174-84233	GT	AGG
(TGA)	 AG	84714-84823	GT	ATG
(GTC)	 AG	84978-85095	GT	GGG
(GGG)	 AG	85271-85408	GT	AGG
(GAA)	 AG	85503-85608	GT	CTG
(ATG)	 AG	85711-85804	GT	CGG
(AGT)	 AG	85931-86031	GT	AGG
(GAT)	 AG	86170-86259	GT	AGG
(AGC)	 AG	86682-86860	GT	CCG
(GTA)	 AG	87256-87358	GT	AGG
(TAC)	 AG	87772-87933	GT	AAG
(GCC)	 AG	88033-88138	GT	AGG
(GCA)	 AG	88247-88355	GT	GGG
(GTA)	 AG	88472-88674	GT	AGG
(GCA)	 AG	88919-89073	GG	AAG
-recovered pasa_asmbl_7880.p1, initial, 85711, 85804
-recovered pasa_asmbl_7880.p1, terminal, 88919, 89073
-recovered pasa_asmbl_7880.p1, internal, 83818, 83942
-recovered pasa_asmbl_7880.p1, internal, 84174, 84233
-recovered pasa_asmbl_7880.p1, internal, 84714, 84823
-recovered pasa_asmbl_7880.p1, internal, 84978, 85095
-recovered pasa_asmbl_7880.p1, internal, 85271, 85408
-recovered pasa_asmbl_7880.p1, internal, 85503, 85608
-recovered pasa_asmbl_7880.p1, internal, 85711, 85804
-recovered pasa_asmbl_7880.p1, internal, 85931, 86031
-recovered pasa_asmbl_7880.p1, internal, 86170, 86259
-recovered pasa_asmbl_7880.p1, internal, 86682, 86860
-recovered pasa_asmbl_7880.p1, internal, 87256, 87358
-recovered pasa_asmbl_7880.p1, internal, 87772, 87933
-recovered pasa_asmbl_7880.p1, internal, 88033, 88138
-recovered pasa_asmbl_7880.p1, internal, 88247, 88355
-recovered pasa_asmbl_7880.p1, internal, 88472, 88674
Valid prediction for GlimmerHMM_glimmerT_30605-T1
Valid prediction for GlimmerHMM_glimmerT_30588-T1
Valid prediction for HiQ_model.g20397.t1
Valid prediction for GlimmerHMM_glimmerT_30598-T1
Valid prediction for snap_scaffold_12-snap.1969-T1
Valid prediction for HiQ_model.g20401.t1
Valid prediction for snap_scaffold_12-snap.1991-T1
Valid prediction for snap_scaffold_12-snap.1994-T1
Valid prediction for snap_scaffold_12-snap.1971-T1
Valid prediction for CodingQuarry_transcript_10340-T1
Valid prediction for snap_scaffold_12-snap.1962-T1
Valid prediction for GlimmerHMM_glimmerT_30585-T1
Valid prediction for Augustus_model.g20392.t1
Valid prediction for GeneMark_model.52864_t
Valid prediction for GlimmerHMM_glimmerT_30597-T1
Valid prediction for Augustus_model.g20393.t1
Valid prediction for Augustus_model.g20394.t1
Valid prediction for Augustus_model.g20410.t1
Valid prediction for Augustus_model.g20405.t1
Valid prediction for GeneMark_model.52849_t
Valid prediction for snap_scaffold_12-snap.1967-T1
Valid prediction for GeneMark_model.52862_t
Valid prediction for Augustus_model.g20399.t1
Valid prediction for Augustus_model.g20406.t1
Valid prediction for GeneMark_model.52867_t
Valid prediction for snap_scaffold_12-snap.1986-T1
Couldn't classify 128764, 128848
Sorry, prediction pasa_asmbl_7874.p1 fails validation.
(CGC)	 TC	128764-128848	GT	TGG
(TGG)	 AG	129175-129253	GT	AGG
(GTT)	 AG	129346-129515	GT	GAG
(GTT)	 AG	129626-129762	GT	AGG
(CTG)	 AG	129911-130030	GT	TGG
(AAA)	 AG	130196-130318	GT	TGG
(CCG)	 AG	130419-130518	GT	AGG
(GAC)	 AG	132336-132435	GT	AGG
(TCG)	 AG	132656-132873	GT	AGG
(GTC)	 AG	132997-133124	GT	CGG
(GGT)	 AG	133208-133291	GT	AGG
(GCT)	 AG	133566-133688	AG	AAA
-recovered pasa_asmbl_7874.p1, terminal, 133566, 133688
-recovered pasa_asmbl_7874.p1, internal, 129175, 129253
-recovered pasa_asmbl_7874.p1, internal, 129346, 129515
-recovered pasa_asmbl_7874.p1, internal, 129626, 129762
-recovered pasa_asmbl_7874.p1, internal, 129911, 130030
-recovered pasa_asmbl_7874.p1, internal, 130196, 130318
-recovered pasa_asmbl_7874.p1, internal, 130419, 130518
-recovered pasa_asmbl_7874.p1, internal, 132336, 132435
-recovered pasa_asmbl_7874.p1, internal, 132656, 132873
-recovered pasa_asmbl_7874.p1, internal, 132997, 133124
-recovered pasa_asmbl_7874.p1, internal, 133208, 133291
Valid prediction for GeneMark_model.52858_t
Valid prediction for GeneMark_model.52842_t
Couldn't classify 58318, 58404
Couldn't classify 59495, 59712
Sorry, prediction pasa_asmbl_7883.p1 fails validation.
(CCG)	 GC	58318-58404	GT	CGG
(GAG)	 AG	58594-58738	GT	CTG
(CGG)	 AG	59495-59712	GA	AGG
-recovered pasa_asmbl_7883.p1, internal, 58594, 58738
Valid prediction for GlimmerHMM_glimmerT_30607-T1
Valid prediction for snap_scaffold_12-snap.1978-T1
Valid prediction for GlimmerHMM_glimmerT_30601-T1
Valid prediction for GeneMark_model.52857_t
Valid prediction for Augustus_model.g20404.t1
Valid prediction for GlimmerHMM_glimmerT_30606-T1
Valid prediction for snap_scaffold_12-snap.1981-T1
Valid prediction for GeneMark_model.52863_t
Valid prediction for GeneMark_model.52844_t
Valid prediction for snap_scaffold_12-snap.1996-T1
Valid prediction for CodingQuarry_transcript_10342-T1
Valid prediction for snap_scaffold_12-snap.1975-T1
Valid prediction for snap_scaffold_12-snap.1989-T1
Valid prediction for snap_scaffold_12-snap.1973-T1
Valid prediction for snap_scaffold_12-snap.1984-T1
Valid prediction for GeneMark_model.52847_t
Valid prediction for GlimmerHMM_glimmerT_30604-T1
Valid prediction for Augustus_model.g20409.t1
Valid prediction for GeneMark_model.52846_t
Valid prediction for GlimmerHMM_glimmerT_30593-T1
Valid prediction for GlimmerHMM_glimmerT_30589-T1
Valid prediction for Augustus_model.g20408.t1
Valid prediction for GeneMark_model.52852_t
Valid prediction for snap_scaffold_12-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_30587-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11693, rend_intergenic: 9787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16536, rend_intergenic: 16301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52310, rend_intergenic: 46313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59724, rend_intergenic: 56829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143360, rend_intergenic: 141167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145232, rend_intergenic: 143607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166358, rend_intergenic: 159934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208885
-exon list size: 536


building trellis

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98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 11693, rend_intergenic: 9787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16536, rend_intergenic: 16301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52310, rend_intergenic: 46313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59724, rend_intergenic: 56829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143360, rend_intergenic: 141167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145232, rend_intergenic: 143607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166358, rend_intergenic: 159934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support