-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_2868999-3194138

-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: +)Couldn't classify 173749, 173926
Sorry, prediction pasa_asmbl_39928.p1 fails validation.
(GCT)	 CA	173749-173926	GT	AGG
(GAA)	 AG	175001-175072	GT	CGG
(GTG)	 AG	176576-176629	GT	CCG
(GCT)	 AG	176886-177074	GT	GGG
(ACA)	 AG	177457-177518	AC	GAA
-recovered pasa_asmbl_39928.p1, terminal, 177457, 177518
-recovered pasa_asmbl_39928.p1, internal, 175001, 175072
-recovered pasa_asmbl_39928.p1, internal, 176576, 176629
-recovered pasa_asmbl_39928.p1, internal, 176886, 177074
Valid prediction for snap_scaffold_3-snap.662-T1
Valid prediction for Augustus_model.g4054.t1
Valid prediction for snap_scaffold_3-snap.652-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6230-T1
Valid prediction for snap_scaffold_3-snap.690-T1
Couldn't classify 189232, 189382
Couldn't classify 191095, 191162
Sorry, prediction pasa_asmbl_39929.p1 fails validation.
(TTT)	 TC	189232-189382	GT	CGG
(CCT)	 AG	190382-190516	GT	AGG
(AAA)	 AG	191095-191162	AC	GGA
-recovered pasa_asmbl_39929.p1, internal, 190382, 190516
Valid prediction for GlimmerHMM_glimmerT_6245-T1
Valid prediction for Augustus_model.g4055.t1
Valid prediction for GlimmerHMM_glimmerT_6239-T1
Valid prediction for snap_scaffold_3-snap.676-T1
Valid prediction for pasa_asmbl_39923.p1
Valid prediction for snap_scaffold_3-snap.678-T1
Valid prediction for snap_scaffold_3-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_6233-T1
Valid prediction for snap_scaffold_3-snap.673-T1
Valid prediction for GlimmerHMM_glimmerT_6235-T1
Valid prediction for CodingQuarry_transcript_46102-T1
Valid prediction for GlimmerHMM_glimmerT_6242-T1
Valid prediction for snap_scaffold_3-snap.677-T1
Valid prediction for GlimmerHMM_glimmerT_6231-T1
Valid prediction for HiQ_model.g4046.t1
Valid prediction for snap_scaffold_3-snap.672-T1
Valid prediction for Augustus_model.g4056.t1
Valid prediction for snap_scaffold_3-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_6224-T1
Valid prediction for snap_scaffold_3-snap.665-T1
Valid prediction for snap_scaffold_3-snap.661-T1
Valid prediction for GlimmerHMM_glimmerT_6246-T1
Valid prediction for GlimmerHMM_glimmerT_6236-T1
Valid prediction for GlimmerHMM_glimmerT_6238-T1
Valid prediction for snap_scaffold_3-snap.689-T1
Valid prediction for GlimmerHMM_glimmerT_6227-T1
Valid prediction for snap_scaffold_3-snap.651-T1
Valid prediction for snap_scaffold_3-snap.675-T1
Valid prediction for snap_scaffold_3-snap.663-T1
Valid prediction for snap_scaffold_3-snap.674-T1
Valid prediction for snap_scaffold_3-snap.683-T1
Valid prediction for snap_scaffold_3-snap.657-T1
Valid prediction for snap_scaffold_3-snap.656-T1
Valid prediction for snap_scaffold_3-snap.696-T1
Couldn't classify 191506, 191558
Sorry, prediction pasa_asmbl_39931.p1 fails validation.
(GGT)	 AT	191506-191558	GT	AAG
(GAG)	 AG	191694-191820	GT	CTG
(ACG)	 AG	192159-192312	GT	GGG
(GCT)	 AG	192403-192463	GT	AAG
(CTG)	 AG	193156-193222	GT	TGG
(GTA)	 AG	193673-193891	GT	AGG
(GGG)	 AG	194421-194462	GT	AGG
(GTT)	 AG	194761-194979	AG	GAA
-recovered pasa_asmbl_39931.p1, terminal, 194761, 194979
-recovered pasa_asmbl_39931.p1, internal, 191694, 191820
-recovered pasa_asmbl_39931.p1, internal, 192159, 192312
-recovered pasa_asmbl_39931.p1, internal, 192403, 192463
-recovered pasa_asmbl_39931.p1, internal, 193156, 193222
-recovered pasa_asmbl_39931.p1, internal, 193673, 193891
-recovered pasa_asmbl_39931.p1, internal, 194421, 194462
Valid prediction for snap_scaffold_3-snap.681-T1
Valid prediction for snap_scaffold_3-snap.664-T1
Valid prediction for Augustus_model.g4061.t1
Valid prediction for snap_scaffold_3-snap.687-T1
Valid prediction for Augustus_model.g4051.t1
Valid prediction for snap_scaffold_3-snap.682-T1
Valid prediction for HiQ_model.g4052.t1
Valid prediction for pasa_asmbl_40816.p1
Valid prediction for snap_scaffold_3-snap.669-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_3-snap.660-T1
Valid prediction for snap_scaffold_3-snap.684-T1
Valid prediction for snap_scaffold_3-snap.659-T1
Valid prediction for Augustus_model.g4058.t1
Couldn't classify 318904, 319239
Sorry, prediction pasa_asmbl_38744.p1 fails validation.
(CTC)	 TG	318904-319239	CT	AGC
Valid prediction for Augustus_model.g4059.t1
Valid prediction for GlimmerHMM_glimmerT_6237-T1
Valid prediction for snap_scaffold_3-snap.680-T1
Valid prediction for GlimmerHMM_glimmerT_6248-T1
Couldn't classify 95929, 95953
Couldn't classify 97389, 97908
Sorry, prediction pasa_asmbl_38752.p1 fails validation.
(GCC)	 CA	95929-95953	GT	TGG
(GGG)	 AG	96266-96379	GT	GGG
(GTG)	 AG	96520-96643	GT	AGG
(AGC)	 AG	97389-97908	AC	CCA
add_exon() Sorry, pasa_asmbl_38752.p1 96520-96643-terminal-3 is invalid.
-recovered pasa_asmbl_38752.p1, terminal, 96520, 96643
-recovered pasa_asmbl_38752.p1, internal, 96266, 96379
-recovered pasa_asmbl_38752.p1, internal, 96520, 96643
Valid prediction for snap_scaffold_3-snap.685-T1
Couldn't classify 13158, 13208
Sorry, prediction pasa_asmbl_38756.p1 fails validation.
(ACA)	 AG	13158-13208	GT	GGG
(GGC)	 AG	13708-13827	GT	CGG
(GGT)	 AG	13983-14045	GT	AGG
(GGG)	 AG	14495-14539	GT	AGG
(GGT)	 AG	15274-15405	GT	TTG
(GAT)	 AG	15656-15724	GT	AGG
(GGT)	 AG	15802-15828	GT	CAG
(GGC)	 AG	15960-16058	GT	AGG
(GGA)	 AG	16224-16259	GT	GAG
(GGA)	 AG	16398-16487	GT	GTG
(TAT)	 AG	16714-16746	GT	AGG
(GGT)	 AG	17169-17204	GT	CTG
(GGC)	 AG	17312-17371	GT	AGG
(GGA)	 AG	17538-17615	GT	AGG
(GGC)	 AG	17805-17840	GT	CTG
(GGT)	 AG	17964-18017	GT	CTG
(GGA)	 AG	18431-18502	GT	CAG
(GGT)	 AG	18726-18791	GT	ACG
(CGA)	 AG	18895-18925	GT	AGG
(CCA)	 AG	19326-19379	GT	AGG
(GTA)	 AG	19491-19525	GT	AAG
(AAC)	 AG	19730-19861	GT	CAG
(GGT)	 AG	20112-20271	GT	CCG
(CCA)	 AG	20385-20449	GT	GGG
(GTG)	 AG	20658-20786	GT	TGG
(CTT)	 AG	20906-20938	GT	TGG
(GAC)	 AG	21134-21478	GT	GAG
(CTG)	 AG	21804-22001	GT	AGG
(GAC)	 AG	22331-22446	GT	TGG
(GCC)	 AG	22734-22947	AG	AGA
-recovered pasa_asmbl_38756.p1, terminal, 22734, 22947
-recovered pasa_asmbl_38756.p1, internal, 13158, 13208
-recovered pasa_asmbl_38756.p1, internal, 13708, 13827
-recovered pasa_asmbl_38756.p1, internal, 13983, 14045
-recovered pasa_asmbl_38756.p1, internal, 14495, 14539
-recovered pasa_asmbl_38756.p1, internal, 15274, 15405
-recovered pasa_asmbl_38756.p1, internal, 15656, 15724
-recovered pasa_asmbl_38756.p1, internal, 15802, 15828
-recovered pasa_asmbl_38756.p1, internal, 15960, 16058
-recovered pasa_asmbl_38756.p1, internal, 16224, 16259
-recovered pasa_asmbl_38756.p1, internal, 16398, 16487
-recovered pasa_asmbl_38756.p1, internal, 16714, 16746
-recovered pasa_asmbl_38756.p1, internal, 17169, 17204
-recovered pasa_asmbl_38756.p1, internal, 17312, 17371
-recovered pasa_asmbl_38756.p1, internal, 17538, 17615
-recovered pasa_asmbl_38756.p1, internal, 17805, 17840
-recovered pasa_asmbl_38756.p1, internal, 17964, 18017
-recovered pasa_asmbl_38756.p1, internal, 18431, 18502
-recovered pasa_asmbl_38756.p1, internal, 18726, 18791
-recovered pasa_asmbl_38756.p1, internal, 18895, 18925
-recovered pasa_asmbl_38756.p1, internal, 19326, 19379
-recovered pasa_asmbl_38756.p1, internal, 19491, 19525
-recovered pasa_asmbl_38756.p1, internal, 19730, 19861
-recovered pasa_asmbl_38756.p1, internal, 20112, 20271
-recovered pasa_asmbl_38756.p1, internal, 20385, 20449
-recovered pasa_asmbl_38756.p1, internal, 20658, 20786
-recovered pasa_asmbl_38756.p1, internal, 20906, 20938
-recovered pasa_asmbl_38756.p1, internal, 21134, 21478
-recovered pasa_asmbl_38756.p1, internal, 21804, 22001
-recovered pasa_asmbl_38756.p1, internal, 22331, 22446
Valid prediction for snap_scaffold_3-snap.654-T1
Valid prediction for snap_scaffold_3-snap.671-T1
Valid prediction for snap_scaffold_3-snap.692-T1
Valid prediction for GlimmerHMM_glimmerT_6240-T1
Valid prediction for snap_scaffold_3-snap.668-T1
Couldn't classify 312396, 312507
Couldn't classify 313473, 313598
Sorry, prediction pasa_asmbl_38746.p1 fails validation.
(CCT)	 AC	312396-312507	GT	GGG
(GAG)	 AG	312663-312811	GT	AGG
(TTC)	 AG	313046-313240	GT	AGG
(GTG)	 AG	313473-313598	CT	CCC
-recovered pasa_asmbl_38746.p1, internal, 312663, 312811
-recovered pasa_asmbl_38746.p1, internal, 313046, 313240
Valid prediction for snap_scaffold_3-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_6226-T1
Valid prediction for Augustus_model.g4048.t1
Couldn't classify 1975, 2283
Sorry, prediction pasa_asmbl_38758.p1 fails validation.
(GAC)	 CA	1975-2283	GA	CCG
Valid prediction for GlimmerHMM_glimmerT_6228-T1
Valid prediction for snap_scaffold_3-snap.691-T1
Valid prediction for GlimmerHMM_glimmerT_6234-T1
Valid prediction for Augustus_model.g4047.t1
Valid prediction for GlimmerHMM_glimmerT_6243-T1
Valid prediction for snap_scaffold_3-snap.694-T1
Valid prediction for snap_scaffold_3-snap.693-T1
Couldn't classify 306430, 306573
Couldn't classify 307324, 307482
Sorry, prediction pasa_asmbl_39782.p1 fails validation.
(CAC)	 GT	306430-306573	GT	AGG
(GTG)	 AG	307324-307482	CT	AGC
Valid prediction for GlimmerHMM_glimmerT_6229-T1
Couldn't classify 10073, 10145
Couldn't classify 12299, 12325
Sorry, prediction pasa_asmbl_38757.p1 fails validation.
(CCT)	 CA	10073-10145	GT	AGG
(GAG)	 AG	11168-11289	GT	AGG
(GGT)	 AG	11750-11776	GT	AGG
(GGT)	 AG	11931-12128	GT	CTG
(GGA)	 AG	12299-12325	GT	CAG
-recovered pasa_asmbl_38757.p1, internal, 11168, 11289
-recovered pasa_asmbl_38757.p1, internal, 11750, 11776
-recovered pasa_asmbl_38757.p1, internal, 11931, 12128
-recovered pasa_asmbl_38757.p1, internal, 12299, 12325
Valid prediction for GlimmerHMM_glimmerT_6244-T1
Valid prediction for CodingQuarry_transcript_46104-T1
Valid prediction for GlimmerHMM_glimmerT_6232-T1
Valid prediction for HiQ_model.g4053.t1
Valid prediction for GlimmerHMM_glimmerT_6225-T1
Couldn't classify 98005, 98412
Sorry, prediction pasa_asmbl_38751.p1 fails validation.
(GGT)	 GG	98005-98412	AC	GAA
Valid prediction for snap_scaffold_3-snap.653-T1
Valid prediction for Augustus_model.g4049.t1
Valid prediction for snap_scaffold_3-snap.655-T1
Valid prediction for CodingQuarry_transcript_46105-T1
Couldn't classify 224832, 224894
Sorry, prediction pasa_asmbl_38748.p1 fails validation.
(GAT)	 CA	224832-224894	GT	AGG
(TTC)	 AG	226922-226993	GT	AGG
(TTT)	 AG	228531-228629	GT	AAG
(GAT)	 AG	229313-229450	GT	GTG
(GCA)	 AG	229808-229924	GT	GGG
(ATT)	 AG	230372-230458	GT	CGG
(GGA)	 AG	231156-231294	GT	AAG
(GGA)	 AG	231611-231705	GT	AGG
(GAG)	 AG	232709-232780	TG	GAT
add_exon() Sorry, pasa_asmbl_38748.p1 231156-231294-terminal-3 is invalid.
-recovered pasa_asmbl_38748.p1, terminal, 231156, 231294
-recovered pasa_asmbl_38748.p1, terminal, 232709, 232780
-recovered pasa_asmbl_38748.p1, internal, 226922, 226993
-recovered pasa_asmbl_38748.p1, internal, 228531, 228629
-recovered pasa_asmbl_38748.p1, internal, 229313, 229450
-recovered pasa_asmbl_38748.p1, internal, 229808, 229924
-recovered pasa_asmbl_38748.p1, internal, 230372, 230458
-recovered pasa_asmbl_38748.p1, internal, 231156, 231294
-recovered pasa_asmbl_38748.p1, internal, 231611, 231705
Valid prediction for Augustus_model.g4050.t1
Valid prediction for GlimmerHMM_glimmerT_6247-T1
Couldn't classify 315206, 315212
Sorry, prediction pasa_asmbl_38745.p1 fails validation.
(CTT)	 TG	315206-315212	GT	GGG
(GAA)	 AG	315473-315642	GT	AGG
(GTG)	 AG	315955-316128	GT	CGG
(CTG)	 AG	316466-316543	TA	AGT
-recovered pasa_asmbl_38745.p1, terminal, 316466, 316543
-recovered pasa_asmbl_38745.p1, internal, 315473, 315642
-recovered pasa_asmbl_38745.p1, internal, 315955, 316128
Valid prediction for snap_scaffold_3-snap.695-T1
Valid prediction for snap_scaffold_3-snap.670-T1
Valid prediction for Augustus_model.g4057.t1
Valid prediction for GlimmerHMM_glimmerT_6241-T1
Couldn't classify 318709, 318747
Couldn't classify 318777, 318993
Couldn't classify 319020, 319078
Sorry, prediction CodingQuarry_transcript_46103-T1 fails validation.
(ATG)	 AA	318709-318747	AA	GGA
(CCC)	 GG	318777-318993	GC	CTG
(ACT)	 CT	319020-319078	TC	AAT
Valid prediction for snap_scaffold_3-snap.697-T1
Valid prediction for snap_scaffold_3-snap.667-T1
Valid prediction for Augustus_model.g4060.t1
Valid prediction for snap_scaffold_3-snap.658-T1
Valid prediction for snap_scaffold_3-snap.686-T1
Valid prediction for Augustus_model.g4063.t1
Valid prediction for HiQ_model.g4062.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31318, rend_intergenic: 22214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150088, rend_intergenic: 147494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231625, rend_intergenic: 228500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268492, rend_intergenic: 266889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 281479, rend_intergenic: 276668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 320784, rend_intergenic: 319304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 325140
-exon list size: 490


building trellis

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74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 31318, rend_intergenic: 22214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150088, rend_intergenic: 147494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231625, rend_intergenic: 228500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268492, rend_intergenic: 266889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 281479, rend_intergenic: 276668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 320784, rend_intergenic: 319304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support