-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_9961134-10156976

-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_23-snap.1939-T1
Valid prediction for snap_scaffold_23-snap.1932-T1
Couldn't classify 18689, 18969
Sorry, prediction pasa_asmbl_31818.p1 fails validation.
(ATG)	 AA	16598-16649	GT	AAG
(GTG)	 AG	18689-18969	CT	ACC
-recovered pasa_asmbl_31818.p1, initial, 16598, 16649
Valid prediction for snap_scaffold_23-snap.1911-T1
Valid prediction for Augustus_model.g34522.t1
Valid prediction for snap_scaffold_23-snap.1918-T1
Valid prediction for snap_scaffold_23-snap.1928-T1
Valid prediction for snap_scaffold_23-snap.1919-T1
Valid prediction for GlimmerHMM_glimmerT_51668-T1
Valid prediction for Augustus_model.g34525.t1
Valid prediction for CodingQuarry_transcript_35781-T1
Couldn't classify 79908, 79979
Sorry, prediction pasa_asmbl_31919.p1 fails validation.
(GGA)	 TA	79908-79979	GT	CAG
(CAG)	 AG	80153-80264	GT	AGG
(GAG)	 AG	80858-80952	GT	AGG
(GAC)	 AG	81260-81373	GT	AGG
(GGC)	 AG	81487-81577	GT	AGG
(TGT)	 AG	81656-81792	GT	TGG
(GCT)	 AG	82105-82198	GT	AGG
(CAT)	 AG	82520-82615	GT	CGG
(TGA)	 AG	82825-82883	GT	AGG
(GGC)	 AG	83140-83262	GT	CGG
(GCG)	 AG	83456-83512	AG	AAA
-recovered pasa_asmbl_31919.p1, terminal, 83456, 83512
-recovered pasa_asmbl_31919.p1, internal, 80153, 80264
-recovered pasa_asmbl_31919.p1, internal, 80858, 80952
-recovered pasa_asmbl_31919.p1, internal, 81260, 81373
-recovered pasa_asmbl_31919.p1, internal, 81487, 81577
-recovered pasa_asmbl_31919.p1, internal, 81656, 81792
-recovered pasa_asmbl_31919.p1, internal, 82105, 82198
-recovered pasa_asmbl_31919.p1, internal, 82520, 82615
-recovered pasa_asmbl_31919.p1, internal, 82825, 82883
-recovered pasa_asmbl_31919.p1, internal, 83140, 83262
Valid prediction for snap_scaffold_23-snap.1921-T1
Couldn't classify 51652, 51684
Couldn't classify 52901, 53005
Sorry, prediction CodingQuarry_transcript_35780-T1 fails validation.
(ATG)	 AC	51652-51684	AT	AAA
(TTG)	 TG	52901-53005	GT	ACG
(GTG)	 AG	53095-53199	GT	AGG
(GCG)	 AG	53748-53867	GT	AGG
(GAG)	 AG	54420-54599	GT	AGG
(GGT)	 AG	55390-55485	GT	AGG
(CTC)	 AG	55899-56042	CC	GAC
-recovered CodingQuarry_transcript_35780-T1, terminal, 55899, 56042
-recovered CodingQuarry_transcript_35780-T1, internal, 53095, 53199
-recovered CodingQuarry_transcript_35780-T1, internal, 53748, 53867
-recovered CodingQuarry_transcript_35780-T1, internal, 54420, 54599
-recovered CodingQuarry_transcript_35780-T1, internal, 55390, 55485
Couldn't classify 86909, 87082
Sorry, prediction pasa_asmbl_31950.p1 fails validation.
(CAG)	 GA	86909-87082	GT	TGG
(GCC)	 AG	87490-87647	GT	GGG
(ATA)	 AG	87904-88033	GT	CGG
(CCT)	 AG	88356-88656	GT	AGG
(GTG)	 AG	89044-89270	GT	AGG
(ATC)	 AG	89561-89689	GT	AGG
(GTG)	 AG	89953-90123	TT	AAT
-recovered pasa_asmbl_31950.p1, terminal, 89953, 90123
-recovered pasa_asmbl_31950.p1, internal, 87490, 87647
-recovered pasa_asmbl_31950.p1, internal, 87904, 88033
-recovered pasa_asmbl_31950.p1, internal, 88356, 88656
-recovered pasa_asmbl_31950.p1, internal, 89044, 89270
-recovered pasa_asmbl_31950.p1, internal, 89561, 89689
Valid prediction for Augustus_model.g34532.t1
Valid prediction for GlimmerHMM_glimmerT_51671-T1
Valid prediction for pasa_asmbl_31823.p1
Couldn't classify 92830, 93015
Sorry, prediction pasa_asmbl_31830.p1 fails validation.
(TTT)	 TG	92830-93015	GT	AGG
(GTG)	 AG	93110-93250	GT	GGG
(AAC)	 AG	93408-93518	GT	TGG
(GCG)	 AG	93851-93955	GA	GAG
-recovered pasa_asmbl_31830.p1, terminal, 93851, 93955
-recovered pasa_asmbl_31830.p1, internal, 93110, 93250
-recovered pasa_asmbl_31830.p1, internal, 93408, 93518
Valid prediction for snap_scaffold_23-snap.1935-T1
Valid prediction for GlimmerHMM_glimmerT_51670-T1
Couldn't classify 9479, 9608
Couldn't classify 9744, 10012
Sorry, prediction pasa_asmbl_31815.p1 fails validation.
(GAC)	 AA	9479-9608	GT	CAG
(ACC)	 AG	9744-10012	TG	GTT
Valid prediction for GlimmerHMM_glimmerT_51658-T1
Valid prediction for GlimmerHMM_glimmerT_51659-T1
Valid prediction for snap_scaffold_23-snap.1916-T1
Valid prediction for pasa_asmbl_31833.p1
Couldn't classify 40036, 40152
Couldn't classify 44776, 44871
Sorry, prediction pasa_asmbl_31820.p1 fails validation.
(CCC)	 AC	40036-40152	GT	AGG
(GTT)	 AG	40361-40413	GT	CTG
(GTA)	 AG	40552-40714	GT	AGG
(GAG)	 AG	41166-41300	GT	AGG
(AAC)	 AG	41485-41625	GT	TGG
(GAG)	 AG	42011-42172	GT	AGG
(ACC)	 AG	43250-43321	GT	AGG
(ATA)	 AG	43422-43677	GT	ATG
(TGC)	 AG	44107-44261	GT	TGG
(ATT)	 AG	44497-44610	GT	AGG
(GTG)	 AG	44776-44871	TG	GGT
-recovered pasa_asmbl_31820.p1, internal, 40361, 40413
-recovered pasa_asmbl_31820.p1, internal, 40552, 40714
-recovered pasa_asmbl_31820.p1, internal, 41166, 41300
-recovered pasa_asmbl_31820.p1, internal, 41485, 41625
-recovered pasa_asmbl_31820.p1, internal, 42011, 42172
-recovered pasa_asmbl_31820.p1, internal, 43250, 43321
-recovered pasa_asmbl_31820.p1, internal, 43422, 43677
-recovered pasa_asmbl_31820.p1, internal, 44107, 44261
-recovered pasa_asmbl_31820.p1, internal, 44497, 44610
Valid prediction for snap_scaffold_23-snap.1912-T1
Valid prediction for snap_scaffold_23-snap.1914-T1
Valid prediction for GlimmerHMM_glimmerT_51669-T1
Valid prediction for snap_scaffold_23-snap.1903-T1
Valid prediction for HiQ_model.g34541.t1
Valid prediction for HiQ_model.g34529.t1
Valid prediction for Augustus_model.g34530.t1
Valid prediction for snap_scaffold_23-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_51661-T1
Valid prediction for snap_scaffold_23-snap.1944-T1
Valid prediction for CodingQuarry_transcript_35782-T1
Couldn't classify 47050, 47223
Couldn't classify 47929, 48051
Sorry, prediction pasa_asmbl_31822.p1 fails validation.
(GTG)	 AG	47050-47223	GT	AGG
(GTG)	 AG	47358-47527	GT	AGG
(TCT)	 AG	47708-47831	GT	AGG
(ACG)	 AG	47929-48051	GT	AGG
-recovered pasa_asmbl_31822.p1, internal, 47050, 47223
-recovered pasa_asmbl_31822.p1, internal, 47358, 47527
-recovered pasa_asmbl_31822.p1, internal, 47708, 47831
-recovered pasa_asmbl_31822.p1, internal, 47929, 48051
Valid prediction for snap_scaffold_23-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_51667-T1
Valid prediction for GlimmerHMM_glimmerT_51665-T1
Valid prediction for HiQ_model.g34531.t1
Valid prediction for GlimmerHMM_glimmerT_51683-T1
Valid prediction for snap_scaffold_23-snap.1909-T1
Valid prediction for snap_scaffold_23-snap.1907-T1
Valid prediction for snap_scaffold_23-snap.1936-T1
Valid prediction for Augustus_model.g34527.t1
Valid prediction for GlimmerHMM_glimmerT_51681-T1
Valid prediction for GlimmerHMM_glimmerT_51674-T1
Valid prediction for GlimmerHMM_glimmerT_51677-T1
Valid prediction for snap_scaffold_23-snap.1905-T1
Valid prediction for GlimmerHMM_glimmerT_51672-T1
Valid prediction for Augustus_model.g34528.t1
Valid prediction for GlimmerHMM_glimmerT_51673-T1
Valid prediction for Augustus_model.g34535.t1
Valid prediction for CodingQuarry_transcript_35783-T1
Valid prediction for snap_scaffold_23-snap.1946-T1
Valid prediction for Augustus_model.g34537.t1
Couldn't classify 86308, 86580
Sorry, prediction pasa_asmbl_31829.p1 fails validation.
(ATG)	 GA	84309-84379	GT	AGG
(ATT)	 AG	84617-84739	GT	GGG
(GTG)	 AG	84871-84937	GT	AGG
(TGG)	 AG	85038-85123	GT	AGG
(AGC)	 AG	85210-85297	GT	AGG
(ACC)	 AG	85508-85595	GT	CCG
(CTG)	 AG	85737-85813	GT	AGG
(GGG)	 AG	85936-86106	GT	AGG
(AGC)	 AG	86308-86580	AT	CCA
-recovered pasa_asmbl_31829.p1, initial, 84309, 84379
-recovered pasa_asmbl_31829.p1, internal, 84617, 84739
-recovered pasa_asmbl_31829.p1, internal, 84871, 84937
-recovered pasa_asmbl_31829.p1, internal, 85038, 85123
-recovered pasa_asmbl_31829.p1, internal, 85210, 85297
-recovered pasa_asmbl_31829.p1, internal, 85508, 85595
-recovered pasa_asmbl_31829.p1, internal, 85737, 85813
-recovered pasa_asmbl_31829.p1, internal, 85936, 86106
Valid prediction for GlimmerHMM_glimmerT_51660-T1
Valid prediction for snap_scaffold_23-snap.1942-T1
Valid prediction for snap_scaffold_23-snap.1917-T1
Valid prediction for snap_scaffold_23-snap.1923-T1
Valid prediction for GlimmerHMM_glimmerT_51663-T1
Valid prediction for snap_scaffold_23-snap.1927-T1
Valid prediction for GlimmerHMM_glimmerT_51656-T1
Valid prediction for GlimmerHMM_glimmerT_51662-T1
Valid prediction for snap_scaffold_23-snap.1934-T1
Valid prediction for Augustus_model.g34524.t1
Valid prediction for snap_scaffold_23-snap.1947-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 GlimmerHMM_glimmerT_51680-T1
Valid prediction for Augustus_model.g34542.t1
Valid prediction for snap_scaffold_23-snap.1938-T1
Valid prediction for snap_scaffold_23-snap.1941-T1
Valid prediction for snap_scaffold_23-snap.1940-T1
Valid prediction for snap_scaffold_23-snap.1929-T1
Valid prediction for snap_scaffold_23-snap.1920-T1
Valid prediction for Augustus_model.g34543.t1
Valid prediction for GlimmerHMM_glimmerT_51679-T1
Valid prediction for snap_scaffold_23-snap.1925-T1
Valid prediction for Augustus_model.g34526.t1
Valid prediction for GlimmerHMM_glimmerT_51664-T1
Valid prediction for Augustus_model.g34534.t1
Valid prediction for snap_scaffold_23-snap.1933-T1
Valid prediction for GlimmerHMM_glimmerT_51682-T1
Valid prediction for GlimmerHMM_glimmerT_51678-T1
Valid prediction for GlimmerHMM_glimmerT_51666-T1
Valid prediction for snap_scaffold_23-snap.1908-T1
Valid prediction for pasa_asmbl_31119.p1
Valid prediction for CodingQuarry_transcript_35779-T1
Valid prediction for GlimmerHMM_glimmerT_51676-T1
Valid prediction for Augustus_model.g34538.t1
Valid prediction for snap_scaffold_23-snap.1913-T1
Valid prediction for snap_scaffold_23-snap.1906-T1
Valid prediction for snap_scaffold_23-snap.1910-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1904-T1
Valid prediction for snap_scaffold_23-snap.1945-T1
Valid prediction for snap_scaffold_23-snap.1931-T1
Couldn't classify 39652, 39717
Couldn't classify 43912, 44043
Sorry, prediction pasa_asmbl_31120.p1 fails validation.
(CTG)	 GT	39652-39717	GT	AGG
(TCT)	 AG	40303-40416	GT	TGG
(ATG)	 AG	41471-41606	GT	GGG
(GAG)	 AG	41813-41907	GT	GGG
(ATC)	 AG	43912-44043	GA	ACG
-recovered pasa_asmbl_31120.p1, initial, 41471, 41606
-recovered pasa_asmbl_31120.p1, internal, 40303, 40416
-recovered pasa_asmbl_31120.p1, internal, 41471, 41606
-recovered pasa_asmbl_31120.p1, internal, 41813, 41907
Valid prediction for Augustus_model.g34540.t1
Valid prediction for Augustus_model.g34536.t1
Valid prediction for Augustus_model.g34539.t1
Valid prediction for snap_scaffold_23-snap.1922-T1
Valid prediction for GlimmerHMM_glimmerT_51675-T1
Valid prediction for snap_scaffold_23-snap.1943-T1
Couldn't classify 32062, 32265
Sorry, prediction pasa_asmbl_31122.p1 fails validation.
(GAC)	 AG	32062-32265	GT	AGG
(GCC)	 AG	33368-33500	GT	GAG
(GTG)	 AG	33900-34141	GT	AGG
(CTG)	 AG	34575-34787	GG	GAG
-recovered pasa_asmbl_31122.p1, terminal, 34575, 34787
-recovered pasa_asmbl_31122.p1, internal, 32062, 32265
-recovered pasa_asmbl_31122.p1, internal, 33368, 33500
-recovered pasa_asmbl_31122.p1, internal, 33900, 34141
Valid prediction for snap_scaffold_23-snap.1930-T1
Couldn't classify 188108, 188198
Sorry, prediction pasa_asmbl_31118.p1 fails validation.
(ACT)	 TT	188108-188198	GC	AGG
(GTT)	 AG	189940-190025	GT	AGG
(TGT)	 AG	191052-191180	CT	AGC
-recovered pasa_asmbl_31118.p1, terminal, 191052, 191180
-recovered pasa_asmbl_31118.p1, internal, 189940, 190025
Valid prediction for GlimmerHMM_glimmerT_51684-T1
Valid prediction for snap_scaffold_23-snap.1937-T1
Valid prediction for Augustus_model.g34533.t1
Couldn't classify 27843, 27990
Couldn't classify 31171, 31310
Sorry, prediction pasa_asmbl_31123.p1 fails validation.
(ATT)	 TG	27843-27990	GT	AGG
(ATT)	 AG	29682-29801	GT	AGG
(GCG)	 AG	29911-30028	GT	CGG
(GAC)	 AG	30501-30679	GT	CGG
(ACA)	 AG	31171-31310	AG	TCA
-recovered pasa_asmbl_31123.p1, internal, 29682, 29801
-recovered pasa_asmbl_31123.p1, internal, 29911, 30028
-recovered pasa_asmbl_31123.p1, internal, 30501, 30679
Valid prediction for Augustus_model.g34523.t1
Valid prediction for GlimmerHMM_glimmerT_51657-T1
Valid prediction for snap_scaffold_23-snap.1915-T1
Sorry, intron length (4) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7433, rend_intergenic: 4860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38575, rend_intergenic: 30103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43327, rend_intergenic: 39335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49652, rend_intergenic: 43401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56073, rend_intergenic: 50972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67883, rend_intergenic: 59319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73279, rend_intergenic: 70207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78714, rend_intergenic: 76660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90123, rend_intergenic: 85932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136499, rend_intergenic: 124823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141827, rend_intergenic: 137571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156312, rend_intergenic: 153886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165745, rend_intergenic: 161100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169908, rend_intergenic: 165812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194099, rend_intergenic: 174935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195843
-exon list size: 432


building trellis

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71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 7433, rend_intergenic: 4860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38575, rend_intergenic: 30103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43327, rend_intergenic: 39335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49652, rend_intergenic: 43401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56073, rend_intergenic: 50972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67883, rend_intergenic: 59319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73279, rend_intergenic: 70207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78714, rend_intergenic: 76660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90123, rend_intergenic: 85932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136499, rend_intergenic: 124823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141827, rend_intergenic: 137571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156312, rend_intergenic: 153886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165745, rend_intergenic: 161100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169908, rend_intergenic: 165812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194099, rend_intergenic: 174935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support