-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_8730318-8944483

-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 18177, 18299
Sorry, prediction pasa_asmbl_50928.p1 fails validation.
(TAC)	 AT	18177-18299	GT	TGG
(GAT)	 AG	18432-18495	GT	GGG
(TAC)	 AG	18951-19072	GT	TGG
(GTG)	 AG	19253-19426	GA	AGG
-recovered pasa_asmbl_50928.p1, terminal, 19253, 19426
-recovered pasa_asmbl_50928.p1, internal, 18432, 18495
-recovered pasa_asmbl_50928.p1, internal, 18951, 19072
Valid prediction for pasa_asmbl_50944.p1
Valid prediction for GeneMark_model.30629_t
Couldn't classify 35881, 36222
Sorry, prediction pasa_asmbl_50933.p1 fails validation.
(ACC)	 CA	35881-36222	GC	CTG
Couldn't classify 109819, 109993
Sorry, prediction pasa_asmbl_50946.p1 fails validation.
(GAT)	 TC	109819-109993	GT	AGG
(AGT)	 AG	110923-110982	GT	GTG
(TCG)	 AG	111136-111320	GT	CAG
(GTG)	 AG	111963-112010	GT	GAG
-recovered pasa_asmbl_50946.p1, terminal, 111963, 112010
-recovered pasa_asmbl_50946.p1, internal, 110923, 110982
-recovered pasa_asmbl_50946.p1, internal, 111136, 111320
-recovered pasa_asmbl_50946.p1, internal, 111963, 112010
Valid prediction for snap_scaffold_7-snap.1761-T1
Valid prediction for CodingQuarry_transcript_57426-T1
Valid prediction for GlimmerHMM_glimmerT_18250-T1
Valid prediction for Augustus_model.g12281.t1
Valid prediction for GlimmerHMM_glimmerT_18264-T1
Valid prediction for GeneMark_model.30608_t
Valid prediction for pasa_asmbl_50950.p1
Valid prediction for snap_scaffold_7-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_18255-T1
Valid prediction for snap_scaffold_7-snap.1755-T1
Valid prediction for GeneMark_model.30607_t
Valid prediction for GlimmerHMM_glimmerT_18259-T1
Valid prediction for CodingQuarry_transcript_57431-T1
Valid prediction for snap_scaffold_7-snap.1745-T1
Valid prediction for GlimmerHMM_glimmerT_18247-T1
Valid prediction for GlimmerHMM_glimmerT_18267-T1
Valid prediction for Augustus_model.g12292.t1
Valid prediction for GeneMark_model.30623_t
Valid prediction for pasa_asmbl_50941.p1
Valid prediction for GlimmerHMM_glimmerT_18274-T1
Valid prediction for snap_scaffold_7-snap.1771-T1
Couldn't classify 37151, 37265
Couldn't classify 39698, 39833
Sorry, prediction pasa_asmbl_50934.p1 fails validation.
(GTG)	 CT	37151-37265	GT	TGG
(CTG)	 AG	38331-38476	GT	TGG
(GCC)	 AG	38602-38724	GT	AGG
(GAG)	 AG	38922-39074	GT	AGG
(ATC)	 AG	39240-39358	GT	GTG
(GCT)	 AG	39698-39833	AC	ACA
-recovered pasa_asmbl_50934.p1, internal, 38331, 38476
-recovered pasa_asmbl_50934.p1, internal, 38602, 38724
-recovered pasa_asmbl_50934.p1, internal, 38922, 39074
-recovered pasa_asmbl_50934.p1, internal, 39240, 39358
Valid prediction for snap_scaffold_7-snap.1753-T1
Valid prediction for snap_scaffold_7-snap.1754-T1
Valid prediction for Augustus_model.g12296.t1
Valid prediction for GlimmerHMM_glimmerT_18271-T1
Valid prediction for GeneMark_model.30604_t
Valid prediction for Augustus_model.g12280.t1
Valid prediction for HiQ_model.g12299.t1
Valid prediction for HiQ_model.g12290.t1
Valid prediction for snap_scaffold_7-snap.1758-T1
Valid prediction for GeneMark_model.30610_t
Valid prediction for CodingQuarry_transcript_57428-T1
Valid prediction for Augustus_model.g12297.t1
Valid prediction for snap_scaffold_7-snap.1764-T1
Valid prediction for snap_scaffold_7-snap.1748-T1
Valid prediction for GeneMark_model.30620_t
Valid prediction for HiQ_model.g12293.t1
Couldn't classify 82279, 82367
Sorry, prediction pasa_asmbl_50943.p1 fails validation.
(AGG)	 GC	82279-82367	GT	AGG
(TTT)	 AG	82496-82561	GT	GAG
(GTG)	 AG	82963-83125	GT	GGG
(CAC)	 AG	83247-83352	GT	CGG
(GTC)	 AG	83866-84033	GT	AGG
(GCT)	 AG	84132-84247	GT	AGG
(ATC)	 AG	84689-84760	GT	CAG
(CAG)	 AG	84921-85085	CT	GAC
-recovered pasa_asmbl_50943.p1, terminal, 82496, 82561
-recovered pasa_asmbl_50943.p1, terminal, 84921, 85085
-recovered pasa_asmbl_50943.p1, internal, 82496, 82561
-recovered pasa_asmbl_50943.p1, internal, 82963, 83125
-recovered pasa_asmbl_50943.p1, internal, 83247, 83352
-recovered pasa_asmbl_50943.p1, internal, 83866, 84033
-recovered pasa_asmbl_50943.p1, internal, 84132, 84247
-recovered pasa_asmbl_50943.p1, internal, 84689, 84760
Valid prediction for pasa_asmbl_50932.p1
Valid prediction for GlimmerHMM_glimmerT_18254-T1
Valid prediction for snap_scaffold_7-snap.1765-T1
Valid prediction for Augustus_model.g12286.t1
Valid prediction for GlimmerHMM_glimmerT_18262-T1
Valid prediction for GeneMark_model.30612_t
Valid prediction for GeneMark_model.30599_t
Valid prediction for GeneMark_model.30627_t
Valid prediction for snap_scaffold_7-snap.1742-T1
Valid prediction for snap_scaffold_7-snap.1757-T1
Valid prediction for GeneMark_model.30618_t
Couldn't classify 40843, 40975
Couldn't classify 44839, 44910
Sorry, prediction pasa_asmbl_50936.p1 fails validation.
(CAG)	 CA	40843-40975	GT	AGG
(AGC)	 AG	41150-41325	GT	AGG
(GTT)	 AG	41445-41479	GT	AGG
(CAT)	 AG	41571-41687	GT	AGG
(CGA)	 AG	41769-41850	GT	CTG
(CAG)	 AG	41949-41977	GT	AGG
(TCT)	 AG	42065-42146	GT	ATG
(GGT)	 AG	42301-42390	GT	AGG
(TCA)	 AG	42500-42592	GT	CAG
(GAG)	 AG	42677-42766	GT	CGG
(GAG)	 AG	42881-42973	GT	AGG
(GCC)	 AG	43064-43135	GT	AGG
(TTG)	 AG	43280-43375	GT	AGG
(CTG)	 AG	43496-43579	GT	TGG
(GTC)	 AG	43687-43773	GT	AGG
(ATG)	 AG	44611-44694	GT	AGG
(GCT)	 AG	44839-44910	AG	GAA
-recovered pasa_asmbl_50936.p1, initial, 44611, 44694
-recovered pasa_asmbl_50936.p1, internal, 41150, 41325
-recovered pasa_asmbl_50936.p1, internal, 41445, 41479
-recovered pasa_asmbl_50936.p1, internal, 41571, 41687
-recovered pasa_asmbl_50936.p1, internal, 41769, 41850
-recovered pasa_asmbl_50936.p1, internal, 41949, 41977
-recovered pasa_asmbl_50936.p1, internal, 42065, 42146
-recovered pasa_asmbl_50936.p1, internal, 42301, 42390
-recovered pasa_asmbl_50936.p1, internal, 42500, 42592
-recovered pasa_asmbl_50936.p1, internal, 42677, 42766
-recovered pasa_asmbl_50936.p1, internal, 42881, 42973
-recovered pasa_asmbl_50936.p1, internal, 43064, 43135
-recovered pasa_asmbl_50936.p1, internal, 43280, 43375
-recovered pasa_asmbl_50936.p1, internal, 43496, 43579
-recovered pasa_asmbl_50936.p1, internal, 43687, 43773
-recovered pasa_asmbl_50936.p1, internal, 44611, 44694
Valid prediction for GlimmerHMM_glimmerT_18244-T1
Valid prediction for GeneMark_model.30600_t
Valid prediction for Augustus_model.g12285.t1
Valid prediction for GeneMark_model.30616_t
Valid prediction for snap_scaffold_7-snap.1768-T1
Valid prediction for Augustus_model.g12282.t1
Couldn't classify 22059, 22976
Sorry, prediction pasa_asmbl_50931.p1 fails validation.
(CCT)	 AG	22059-22976	AA	AGA
Valid prediction for GeneMark_model.30601_t
Valid prediction for snap_scaffold_7-snap.1741-T1
Couldn't classify 82004, 82114
Sorry, prediction pasa_asmbl_51538.p1 fails validation.
(ATG)	 GA	75971-76008	GT	TAG
(CGT)	 AG	77756-77846	GT	CAG
(GGC)	 AG	77993-78030	GT	AAG
(GGA)	 AG	78145-78287	GT	AGG
(AAA)	 AG	78997-79048	GT	GAG
(CAA)	 AG	79170-79278	GT	TGG
(GTG)	 AG	79495-79565	GT	GAG
(GAA)	 AG	80433-80513	GT	AGG
(GAA)	 AG	80675-80798	GT	AGG
(GAG)	 AG	81119-81252	GT	ATG
(AAT)	 AG	81404-81541	GT	TGG
(GGA)	 AG	81674-81827	GT	ACG
(AAT)	 AG	82004-82114	CT	CTC
-recovered pasa_asmbl_51538.p1, initial, 75971, 76008
add_exon() Sorry, pasa_asmbl_51538.p1 78145-78287-terminal-2 is invalid.
-recovered pasa_asmbl_51538.p1, terminal, 78145, 78287
-recovered pasa_asmbl_51538.p1, terminal, 79495, 79565
-recovered pasa_asmbl_51538.p1, internal, 77756, 77846
-recovered pasa_asmbl_51538.p1, internal, 77993, 78030
-recovered pasa_asmbl_51538.p1, internal, 78145, 78287
-recovered pasa_asmbl_51538.p1, internal, 78997, 79048
-recovered pasa_asmbl_51538.p1, internal, 79170, 79278
-recovered pasa_asmbl_51538.p1, internal, 79495, 79565
-recovered pasa_asmbl_51538.p1, internal, 80433, 80513
-recovered pasa_asmbl_51538.p1, internal, 80675, 80798
-recovered pasa_asmbl_51538.p1, internal, 81119, 81252
-recovered pasa_asmbl_51538.p1, internal, 81404, 81541
-recovered pasa_asmbl_51538.p1, internal, 81674, 81827
Valid prediction for HiQ_model.g12284.t1
Valid prediction for CodingQuarry_transcript_57424-T1
Valid prediction for GlimmerHMM_glimmerT_18256-T1
Valid prediction for GlimmerHMM_glimmerT_18248-T1
Valid prediction for GlimmerHMM_glimmerT_18249-T1
Valid prediction for GeneMark_model.30617_t
Valid prediction for snap_scaffold_7-snap.1762-T1
Valid prediction for snap_scaffold_7-snap.1747-T1
Couldn't classify 130023, 130094
Sorry, prediction pasa_asmbl_50951.p1 fails validation.
(ACA)	 CC	130023-130094	GT	AAG
(GAC)	 AG	130404-130541	GT	AGG
(CTG)	 AG	130863-130929	GT	GAG
(TGT)	 AG	131036-131091	GT	TGG
(GAG)	 AG	131367-131615	CT	GAC
-recovered pasa_asmbl_50951.p1, terminal, 131367, 131615
-recovered pasa_asmbl_50951.p1, internal, 130404, 130541
-recovered pasa_asmbl_50951.p1, internal, 130863, 130929
-recovered pasa_asmbl_50951.p1, internal, 131036, 131091
Valid prediction for GlimmerHMM_glimmerT_18243-T1
Valid prediction for GlimmerHMM_glimmerT_18258-T1
Valid prediction for HiQ_model.g12302.t1
Couldn't classify 21177, 21422
Sorry, prediction pasa_asmbl_50930.p1 fails validation.
(ATG)	 AA	20427-20483	GT	AGG
(CTG)	 AG	20706-20874	GT	AGG
(TGC)	 AG	20958-21019	GT	AGG
(TCC)	 AG	21177-21422	TG	GAT
-recovered pasa_asmbl_50930.p1, initial, 20427, 20483
-recovered pasa_asmbl_50930.p1, internal, 20706, 20874
-recovered pasa_asmbl_50930.p1, internal, 20958, 21019
Valid prediction for GlimmerHMM_glimmerT_18245-T1
Valid prediction for GeneMark_model.30602_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 pasa_asmbl_49848.p1
Valid prediction for GlimmerHMM_glimmerT_18251-T1
Valid prediction for GeneMark_model.30606_t
Valid prediction for snap_scaffold_7-snap.1751-T1
Valid prediction for Augustus_model.g12294.t1
Valid prediction for pasa_asmbl_50357.p1
Valid prediction for snap_scaffold_7-snap.1767-T1
Valid prediction for snap_scaffold_7-snap.1750-T1
Valid prediction for snap_scaffold_7-snap.1763-T1
Valid prediction for Augustus_model.g12301.t1
Valid prediction for GeneMark_model.30609_t
Valid prediction for GeneMark_model.30628_t
Valid prediction for HiQ_model.g12298.t1
Valid prediction for snap_scaffold_7-snap.1766-T1
Valid prediction for Augustus_model.g12289.t1
Valid prediction for GlimmerHMM_glimmerT_18261-T1
Valid prediction for GlimmerHMM_glimmerT_18252-T1
Valid prediction for snap_scaffold_7-snap.1756-T1
Valid prediction for GeneMark_model.30625_t
Valid prediction for GlimmerHMM_glimmerT_18273-T1
Valid prediction for snap_scaffold_7-snap.1769-T1
Valid prediction for CodingQuarry_transcript_57427-T1
Valid prediction for GlimmerHMM_glimmerT_18272-T1
Valid prediction for GlimmerHMM_glimmerT_18246-T1
Valid prediction for Augustus_model.g12303.t1
Valid prediction for GeneMark_model.30614_t
Valid prediction for snap_scaffold_7-snap.1746-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.30626_t
Valid prediction for GeneMark_model.30603_t
Valid prediction for GlimmerHMM_glimmerT_18266-T1
Valid prediction for pasa_asmbl_49847.p1
Valid prediction for GlimmerHMM_glimmerT_18270-T1
Valid prediction for pasa_asmbl_49849.p1
Valid prediction for GeneMark_model.30630_t
Valid prediction for snap_scaffold_7-snap.1752-T1
Valid prediction for snap_scaffold_7-snap.1759-T1
Couldn't classify 28277, 28813
Sorry, prediction pasa_asmbl_49852.p1 fails validation.
(ACT)	 TA	28277-28813	GG	GAG
Valid prediction for snap_scaffold_7-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_18263-T1
Valid prediction for GlimmerHMM_glimmerT_18257-T1
Valid prediction for GeneMark_model.30615_t
Valid prediction for CodingQuarry_transcript_57430-T1
Valid prediction for snap_scaffold_7-snap.1760-T1
Valid prediction for Augustus_model.g12300.t1
Valid prediction for snap_scaffold_7-snap.1749-T1
Valid prediction for GeneMark_model.30622_t
Valid prediction for GeneMark_model.30611_t
Valid prediction for snap_scaffold_7-snap.1770-T1
Valid prediction for GeneMark_model.30619_t
Valid prediction for Augustus_model.g12283.t1
Couldn't classify 189432, 189675
Couldn't classify 190342, 190458
Sorry, prediction pasa_asmbl_49846.p1 fails validation.
(CCC)	 TA	189432-189675	GT	AAG
(ATC)	 AG	189762-190005	GT	AGG
(GGG)	 AG	190120-190252	GT	AGG
(GTG)	 AG	190342-190458	TA	AAT
-recovered pasa_asmbl_49846.p1, internal, 189762, 190005
-recovered pasa_asmbl_49846.p1, internal, 190120, 190252
Valid prediction for Augustus_model.g12295.t1
Valid prediction for GlimmerHMM_glimmerT_18253-T1
Valid prediction for snap_scaffold_7-snap.1744-T1
Valid prediction for GeneMark_model.30621_t
Valid prediction for GlimmerHMM_glimmerT_18260-T1
Valid prediction for snap_scaffold_7-snap.1773-T1
Valid prediction for CodingQuarry_transcript_57429-T1
Valid prediction for GeneMark_model.30624_t
Valid prediction for GlimmerHMM_glimmerT_18265-T1
Valid prediction for snap_scaffold_7-snap.1772-T1
Valid prediction for HiQ_model.g12287.t1
Valid prediction for GeneMark_model.30605_t
Valid prediction for GlimmerHMM_glimmerT_18268-T1
Valid prediction for GlimmerHMM_glimmerT_18269-T1
Valid prediction for snap_scaffold_7-snap.1775-T1
Valid prediction for HiQ_model.g12291.t1
Valid prediction for Augustus_model.g12288.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39928, rend_intergenic: 35791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85085, rend_intergenic: 73772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214166
-exon list size: 542


building trellis

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68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 39928, rend_intergenic: 35791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85085, rend_intergenic: 73772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 203942 - 214166
-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
GOT 5prime partial gene.

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