-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_1876168-2275228

-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_21-snap.381-T1
Valid prediction for GeneMark_model.84046_t
Valid prediction for snap_scaffold_21-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_48349-T1
Valid prediction for Augustus_model.g32340.t1
Valid prediction for snap_scaffold_21-snap.379-T1
Valid prediction for Augustus_model.g32336.t1
Valid prediction for GeneMark_model.84048_t
Valid prediction for snap_scaffold_21-snap.357-T1
Valid prediction for GlimmerHMM_glimmerT_48360-T1
Valid prediction for snap_scaffold_21-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_48358-T1
Valid prediction for GlimmerHMM_glimmerT_48356-T1
Valid prediction for GlimmerHMM_glimmerT_48357-T1
Valid prediction for snap_scaffold_21-snap.354-T1
Valid prediction for GeneMark_model.84043_t
Valid prediction for HiQ_model.g32353.t1
Valid prediction for Augustus_model.g32335.t1
Valid prediction for GlimmerHMM_glimmerT_48350-T1
Valid prediction for GeneMark_model.84060_t
Valid prediction for snap_scaffold_21-snap.344-T1
Valid prediction for GeneMark_model.84049_t
Valid prediction for GlimmerHMM_glimmerT_48378-T1
Valid prediction for snap_scaffold_21-snap.378-T1
Valid prediction for GeneMark_model.84041_t
Valid prediction for GlimmerHMM_glimmerT_48368-T1
Valid prediction for GlimmerHMM_glimmerT_48348-T1
Valid prediction for GeneMark_model.84044_t
Valid prediction for GlimmerHMM_glimmerT_48363-T1
Valid prediction for snap_scaffold_21-snap.356-T1
Valid prediction for GeneMark_model.84063_t
Valid prediction for CodingQuarry_transcript_32398-T1
Valid prediction for GlimmerHMM_glimmerT_48361-T1
Couldn't classify 386448, 386690
Sorry, prediction pasa_asmbl_28393.p1 fails validation.
(AAA)	 AG	386448-386690	GT	AGG
(ACT)	 AG	386859-387028	GT	AAG
(GAC)	 AG	387742-387867	GT	AGG
(GTT)	 AG	388072-388158	GT	GGG
(GCG)	 AG	388329-388502	GT	AGG
(TGG)	 AG	389366-389555	GT	GGG
(GCT)	 AG	390128-390281	GT	AGG
(ACC)	 AG	390443-390541	GT	CGG
(ATG)	 AG	391086-391176	GT	AGG
(CAT)	 AG	391477-391581	GT	CTG
(GAA)	 AG	391787-391939	GT	AGG
(GGC)	 AG	392647-392769	GT	AGG
(GGT)	 AG	392905-392970	GT	AGG
(GAA)	 AG	393816-393896	GT	AGG
(GGT)	 AG	394038-394164	GT	AGG
(GTG)	 AG	394404-394522	GT	CAG
(GGG)	 AG	395414-395477	GT	GAG
-recovered pasa_asmbl_28393.p1, initial, 391086, 391176
-recovered pasa_asmbl_28393.p1, terminal, 395414, 395477
-recovered pasa_asmbl_28393.p1, internal, 386448, 386690
-recovered pasa_asmbl_28393.p1, internal, 386859, 387028
-recovered pasa_asmbl_28393.p1, internal, 387742, 387867
-recovered pasa_asmbl_28393.p1, internal, 388072, 388158
-recovered pasa_asmbl_28393.p1, internal, 388329, 388502
-recovered pasa_asmbl_28393.p1, internal, 389366, 389555
-recovered pasa_asmbl_28393.p1, internal, 390128, 390281
-recovered pasa_asmbl_28393.p1, internal, 390443, 390541
-recovered pasa_asmbl_28393.p1, internal, 391086, 391176
-recovered pasa_asmbl_28393.p1, internal, 391477, 391581
-recovered pasa_asmbl_28393.p1, internal, 391787, 391939
-recovered pasa_asmbl_28393.p1, internal, 392647, 392769
-recovered pasa_asmbl_28393.p1, internal, 392905, 392970
-recovered pasa_asmbl_28393.p1, internal, 393816, 393896
-recovered pasa_asmbl_28393.p1, internal, 394038, 394164
-recovered pasa_asmbl_28393.p1, internal, 394404, 394522
-recovered pasa_asmbl_28393.p1, internal, 395414, 395477
Valid prediction for GlimmerHMM_glimmerT_48366-T1
Valid prediction for GeneMark_model.84051_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 CodingQuarry_transcript_32396-T1
Valid prediction for snap_scaffold_21-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_48367-T1
Valid prediction for GlimmerHMM_glimmerT_48362-T1
Valid prediction for snap_scaffold_21-snap.366-T1
Valid prediction for snap_scaffold_21-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_48355-T1
Valid prediction for GeneMark_model.84038_t
Valid prediction for GeneMark_model.84052_t
Valid prediction for pasa_asmbl_27466.p1
Valid prediction for GeneMark_model.84047_t
Valid prediction for snap_scaffold_21-snap.359-T1
Valid prediction for snap_scaffold_21-snap.350-T1
Valid prediction for GlimmerHMM_glimmerT_48347-T1
Valid prediction for snap_scaffold_21-snap.365-T1
Couldn't classify 87026, 87049
Couldn't classify 92193, 92237
Sorry, prediction pasa_asmbl_28175.p1 fails validation.
(GGC)	 GC	87026-87049	GT	TGG
(TTG)	 AG	87879-88076	GT	AGG
(TAC)	 AG	88983-89086	GT	AGG
(GAA)	 AG	89229-89289	GT	AGG
(GGC)	 AG	91331-91381	GT	AGG
(CAA)	 AG	92193-92237	GA	ATG
-recovered pasa_asmbl_28175.p1, internal, 87879, 88076
-recovered pasa_asmbl_28175.p1, internal, 88983, 89086
-recovered pasa_asmbl_28175.p1, internal, 89229, 89289
-recovered pasa_asmbl_28175.p1, internal, 91331, 91381
Valid prediction for snap_scaffold_21-snap.362-T1
Valid prediction for snap_scaffold_21-snap.352-T1
Valid prediction for snap_scaffold_21-snap.364-T1
Valid prediction for snap_scaffold_21-snap.368-T1
Valid prediction for GeneMark_model.84037_t
Valid prediction for Augustus_model.g32349.t1
Valid prediction for snap_scaffold_21-snap.376-T1
Valid prediction for pasa_asmbl_27458.p1
Valid prediction for GeneMark_model.84054_t
Valid prediction for snap_scaffold_21-snap.355-T1
Valid prediction for snap_scaffold_21-snap.373-T1
Valid prediction for snap_scaffold_21-snap.375-T1
Valid prediction for snap_scaffold_21-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_48365-T1
Valid prediction for Augustus_model.g32339.t1
Valid prediction for GeneMark_model.84058_t
Valid prediction for snap_scaffold_21-snap.348-T1
Valid prediction for snap_scaffold_21-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_48375-T1
Valid prediction for snap_scaffold_21-snap.377-T1
Couldn't classify 93541, 93595
Sorry, prediction pasa_asmbl_27463.p1 fails validation.
(AAG)	 AA	93541-93595	GT	TGG
(CCT)	 AG	93834-93990	GT	AGG
(GAG)	 AG	94969-95128	GT	TGG
(GGC)	 AG	95427-95615	GT	CGG
(GTA)	 AG	96090-96152	GT	ATG
(GAG)	 AG	96532-96543	TC	GAT
-recovered pasa_asmbl_27463.p1, terminal, 96532, 96543
-recovered pasa_asmbl_27463.p1, internal, 93834, 93990
-recovered pasa_asmbl_27463.p1, internal, 94969, 95128
-recovered pasa_asmbl_27463.p1, internal, 95427, 95615
-recovered pasa_asmbl_27463.p1, internal, 96090, 96152
Valid prediction for Augustus_model.g32344.t1
Valid prediction for snap_scaffold_21-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_48369-T1
Valid prediction for GeneMark_model.84045_t
Valid prediction for GlimmerHMM_glimmerT_48351-T1
Valid prediction for GeneMark_model.84064_t
Valid prediction for snap_scaffold_21-snap.349-T1
Valid prediction for Augustus_model.g32346.t1
Couldn't classify 102693, 102821
Sorry, prediction pasa_asmbl_27459.p1 fails validation.
(ACC)	 GA	102693-102821	GT	TGG
(TGC)	 AG	103079-103220	GT	CCG
(GGG)	 AG	103458-103634	GT	CAG
(GTG)	 AG	104015-104198	GT	AGG
(ATC)	 AG	104466-104785	GT	CGG
(GTG)	 AG	105371-105466	GT	AGG
(AAA)	 AG	106295-106378	GT	CGG
(CTG)	 AG	106786-106969	GT	AGG
(AAT)	 AG	107801-107826	GT	AGG
(CTG)	 AG	107989-108115	GT	AGG
(ATC)	 AG	108354-108397	GT	TGG
(GCC)	 AG	108632-108712	GT	AGG
(ATG)	 AG	109369-109470	GT	AGG
(CTG)	 AG	110775-110828	GT	AGG
(GAA)	 AG	110958-111035	GT	TGG
(CTG)	 AG	111219-111402	GT	AGG
(GCC)	 AG	111507-111568	GT	AGG
(ACC)	 AG	111798-111860	GT	AGG
(ACT)	 AG	112033-112300	GT	AGG
(ACC)	 AG	112448-112476	GT	AGG
(CTC)	 AG	112585-112632	GT	TGG
(ATG)	 AG	112752-112829	GT	TGG
(GTG)	 AG	112957-113149	GT	CAG
(GCC)	 AG	113351-113388	GT	AGG
(AAG)	 AG	113467-113576	GT	TGG
(CAG)	 AG	114366-114434	TG	AAT
-recovered pasa_asmbl_27459.p1, initial, 109369, 109470
add_exon() Sorry, pasa_asmbl_27459.p1 112752-112829-initial-1 is invalid.
-recovered pasa_asmbl_27459.p1, initial, 112752, 112829
-recovered pasa_asmbl_27459.p1, terminal, 114366, 114434
-recovered pasa_asmbl_27459.p1, internal, 103079, 103220
-recovered pasa_asmbl_27459.p1, internal, 103458, 103634
-recovered pasa_asmbl_27459.p1, internal, 104015, 104198
-recovered pasa_asmbl_27459.p1, internal, 104466, 104785
-recovered pasa_asmbl_27459.p1, internal, 105371, 105466
-recovered pasa_asmbl_27459.p1, internal, 106295, 106378
-recovered pasa_asmbl_27459.p1, internal, 106786, 106969
-recovered pasa_asmbl_27459.p1, internal, 107801, 107826
-recovered pasa_asmbl_27459.p1, internal, 107989, 108115
-recovered pasa_asmbl_27459.p1, internal, 108354, 108397
-recovered pasa_asmbl_27459.p1, internal, 108632, 108712
-recovered pasa_asmbl_27459.p1, internal, 109369, 109470
-recovered pasa_asmbl_27459.p1, internal, 110775, 110828
-recovered pasa_asmbl_27459.p1, internal, 110958, 111035
-recovered pasa_asmbl_27459.p1, internal, 111219, 111402
-recovered pasa_asmbl_27459.p1, internal, 111507, 111568
-recovered pasa_asmbl_27459.p1, internal, 111798, 111860
-recovered pasa_asmbl_27459.p1, internal, 112033, 112300
-recovered pasa_asmbl_27459.p1, internal, 112448, 112476
-recovered pasa_asmbl_27459.p1, internal, 112585, 112632
-recovered pasa_asmbl_27459.p1, internal, 112752, 112829
-recovered pasa_asmbl_27459.p1, internal, 112957, 113149
-recovered pasa_asmbl_27459.p1, internal, 113351, 113388
-recovered pasa_asmbl_27459.p1, internal, 113467, 113576
Valid prediction for GeneMark_model.84050_t
Valid prediction for Augustus_model.g32348.t1
Valid prediction for GeneMark_model.84033_t
Valid prediction for GeneMark_model.84040_t
Valid prediction for GeneMark_model.84059_t
Valid prediction for HiQ_model.g32342.t1
Valid prediction for GeneMark_model.84035_t
Valid prediction for Augustus_model.g32341.t1
Valid prediction for CodingQuarry_transcript_32397-T1
Valid prediction for GlimmerHMM_glimmerT_48364-T1
Valid prediction for snap_scaffold_21-snap.343-T1
Valid prediction for snap_scaffold_21-snap.345-T1
Valid prediction for GlimmerHMM_glimmerT_48373-T1
Valid prediction for GlimmerHMM_glimmerT_48374-T1
Valid prediction for snap_scaffold_21-snap.372-T1
Valid prediction for GeneMark_model.84032_t
Valid prediction for GeneMark_model.84055_t
Valid prediction for HiQ_model.g32343.t1
Valid prediction for GlimmerHMM_glimmerT_48359-T1
Valid prediction for snap_scaffold_21-snap.374-T1
Couldn't classify 26096, 26179
Sorry, prediction pasa_asmbl_27467.p1 fails validation.
(GAG)	 CA	26096-26179	GT	AGG
(AAC)	 AG	28635-29183	CT	AAC
-recovered pasa_asmbl_27467.p1, terminal, 28635, 29183
Valid prediction for snap_scaffold_21-snap.371-T1
Valid prediction for GeneMark_model.84039_t
Valid prediction for snap_scaffold_21-snap.351-T1
Valid prediction for snap_scaffold_21-snap.347-T1
Valid prediction for GlimmerHMM_glimmerT_48372-T1
Valid prediction for Augustus_model.g32345.t1
Valid prediction for Augustus_model.g32347.t1
Valid prediction for GlimmerHMM_glimmerT_48352-T1
Valid prediction for GlimmerHMM_glimmerT_48353-T1
Valid prediction for Augustus_model.g32337.t1
Couldn't classify 40892, 41060
Couldn't classify 42037, 42055
Sorry, prediction pasa_asmbl_28242.p1 fails validation.
(GTT)	 TA	40892-41060	GT	CGG
(GTG)	 AG	41265-41496	GT	AAG
(ATT)	 AG	41620-41702	GT	TAG
(TGA)	 AG	41801-41930	GT	TGG
(TTG)	 AG	42037-42055	CA	CAC
add_exon() Sorry, pasa_asmbl_28242.p1 41265-41496-terminal-3 is invalid.
-recovered pasa_asmbl_28242.p1, terminal, 41265, 41496
-recovered pasa_asmbl_28242.p1, internal, 41265, 41496
-recovered pasa_asmbl_28242.p1, internal, 41620, 41702
-recovered pasa_asmbl_28242.p1, internal, 41801, 41930
Valid prediction for GeneMark_model.84036_t
Valid prediction for snap_scaffold_21-snap.380-T1
Valid prediction for GeneMark_model.84062_t
Valid prediction for Augustus_model.g32352.t1
Valid prediction for snap_scaffold_21-snap.367-T1
Valid prediction for GeneMark_model.84053_t
Valid prediction for GlimmerHMM_glimmerT_48370-T1
Valid prediction for GlimmerHMM_glimmerT_48376-T1
Valid prediction for GeneMark_model.84057_t
Valid prediction for GeneMark_model.84056_t
Valid prediction for Augustus_model.g32338.t1
Valid prediction for GeneMark_model.84042_t
Valid prediction for HiQ_model.g32350.t1
Valid prediction for snap_scaffold_21-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_48371-T1
Valid prediction for GlimmerHMM_glimmerT_48354-T1
Valid prediction for pasa_asmbl_27457.p1
Valid prediction for HiQ_model.g32351.t1
Valid prediction for GlimmerHMM_glimmerT_48377-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 278863, rend_intergenic: 277714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 393299, rend_intergenic: 391063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 399061
-exon list size: 472


building trellis

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90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 278863, rend_intergenic: 277714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 393299, rend_intergenic: 391063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17442
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 16900
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 4114 - 16900
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 5956 - 16900
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 6221 - 16900