-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_8730318-8946129

-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 82279, 82367
Sorry, prediction pasa_asmbl_50058.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_50058.p1, terminal, 82496, 82561
-recovered pasa_asmbl_50058.p1, terminal, 84921, 85085
-recovered pasa_asmbl_50058.p1, internal, 82496, 82561
-recovered pasa_asmbl_50058.p1, internal, 82963, 83125
-recovered pasa_asmbl_50058.p1, internal, 83247, 83352
-recovered pasa_asmbl_50058.p1, internal, 83866, 84033
-recovered pasa_asmbl_50058.p1, internal, 84132, 84247
-recovered pasa_asmbl_50058.p1, internal, 84689, 84760
Valid prediction for snap_scaffold_7-snap.1741-T1
Valid prediction for snap_scaffold_7-snap.1728-T1
Valid prediction for snap_scaffold_7-snap.1732-T1
Valid prediction for snap_scaffold_7-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_17825-T1
Valid prediction for Augustus_model.g11956.t1
Valid prediction for Augustus_model.g11971.t1
Valid prediction for snap_scaffold_7-snap.1730-T1
Valid prediction for snap_scaffold_7-snap.1738-T1
Valid prediction for GlimmerHMM_glimmerT_17816-T1
Valid prediction for GlimmerHMM_glimmerT_17823-T1
Valid prediction for GlimmerHMM_glimmerT_17836-T1
Valid prediction for HiQ_model.g11977.t1
Couldn't classify 35881, 36222
Sorry, prediction pasa_asmbl_50048.p1 fails validation.
(ACC)	 CA	35881-36222	GC	CTG
Valid prediction for pasa_asmbl_50047.p1
Couldn't classify 82004, 82114
Sorry, prediction pasa_asmbl_50653.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_50653.p1, initial, 75971, 76008
add_exon() Sorry, pasa_asmbl_50653.p1 78145-78287-terminal-2 is invalid.
-recovered pasa_asmbl_50653.p1, terminal, 78145, 78287
-recovered pasa_asmbl_50653.p1, terminal, 79495, 79565
-recovered pasa_asmbl_50653.p1, internal, 77756, 77846
-recovered pasa_asmbl_50653.p1, internal, 77993, 78030
-recovered pasa_asmbl_50653.p1, internal, 78145, 78287
-recovered pasa_asmbl_50653.p1, internal, 78997, 79048
-recovered pasa_asmbl_50653.p1, internal, 79170, 79278
-recovered pasa_asmbl_50653.p1, internal, 79495, 79565
-recovered pasa_asmbl_50653.p1, internal, 80433, 80513
-recovered pasa_asmbl_50653.p1, internal, 80675, 80798
-recovered pasa_asmbl_50653.p1, internal, 81119, 81252
-recovered pasa_asmbl_50653.p1, internal, 81404, 81541
-recovered pasa_asmbl_50653.p1, internal, 81674, 81827
Valid prediction for GlimmerHMM_glimmerT_17813-T1
Valid prediction for GlimmerHMM_glimmerT_17814-T1
Couldn't classify 37151, 37265
Couldn't classify 39698, 39833
Sorry, prediction pasa_asmbl_50049.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_50049.p1, internal, 38331, 38476
-recovered pasa_asmbl_50049.p1, internal, 38602, 38724
-recovered pasa_asmbl_50049.p1, internal, 38922, 39074
-recovered pasa_asmbl_50049.p1, internal, 39240, 39358
Couldn't classify 22059, 22976
Sorry, prediction pasa_asmbl_50046.p1 fails validation.
(CCT)	 AG	22059-22976	AA	AGA
Valid prediction for pasa_asmbl_50056.p1
Couldn't classify 109819, 109993
Sorry, prediction pasa_asmbl_50062.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_50062.p1, terminal, 111963, 112010
-recovered pasa_asmbl_50062.p1, internal, 110923, 110982
-recovered pasa_asmbl_50062.p1, internal, 111136, 111320
-recovered pasa_asmbl_50062.p1, internal, 111963, 112010
Valid prediction for GlimmerHMM_glimmerT_17821-T1
Valid prediction for snap_scaffold_7-snap.1737-T1
Couldn't classify 20373, 20483
Couldn't classify 21177, 21422
Sorry, prediction pasa_asmbl_50045.p1 fails validation.
(CAA)	 AT	20373-20483	GT	AGG
(CTG)	 AG	20706-20874	GT	AGG
(TGC)	 AG	20958-21019	GT	AGG
(TCC)	 AG	21177-21422	TG	GAT
-recovered pasa_asmbl_50045.p1, internal, 20706, 20874
-recovered pasa_asmbl_50045.p1, internal, 20958, 21019
Valid prediction for snap_scaffold_7-snap.1745-T1
Valid prediction for HiQ_model.g11974.t1
Valid prediction for pasa_asmbl_50067.p1
Valid prediction for HiQ_model.g11968.t1
Valid prediction for Augustus_model.g11957.t1
Valid prediction for Augustus_model.g11960.t1
Valid prediction for snap_scaffold_7-snap.1726-T1
Valid prediction for snap_scaffold_7-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_17827-T1
Valid prediction for GlimmerHMM_glimmerT_17828-T1
Valid prediction for GlimmerHMM_glimmerT_17817-T1
Valid prediction for GlimmerHMM_glimmerT_17830-T1
Valid prediction for snap_scaffold_7-snap.1747-T1
Valid prediction for HiQ_model.g11965.t1
Valid prediction for snap_scaffold_7-snap.1759-T1
Couldn't classify 40843, 40975
Sorry, prediction pasa_asmbl_50051.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	44839-44919	GA	GAG
-recovered pasa_asmbl_50051.p1, initial, 44611, 44694
-recovered pasa_asmbl_50051.p1, terminal, 44839, 44919
-recovered pasa_asmbl_50051.p1, internal, 41150, 41325
-recovered pasa_asmbl_50051.p1, internal, 41445, 41479
-recovered pasa_asmbl_50051.p1, internal, 41571, 41687
-recovered pasa_asmbl_50051.p1, internal, 41769, 41850
-recovered pasa_asmbl_50051.p1, internal, 41949, 41977
-recovered pasa_asmbl_50051.p1, internal, 42065, 42146
-recovered pasa_asmbl_50051.p1, internal, 42301, 42390
-recovered pasa_asmbl_50051.p1, internal, 42500, 42592
-recovered pasa_asmbl_50051.p1, internal, 42677, 42766
-recovered pasa_asmbl_50051.p1, internal, 42881, 42973
-recovered pasa_asmbl_50051.p1, internal, 43064, 43135
-recovered pasa_asmbl_50051.p1, internal, 43280, 43375
-recovered pasa_asmbl_50051.p1, internal, 43496, 43579
-recovered pasa_asmbl_50051.p1, internal, 43687, 43773
-recovered pasa_asmbl_50051.p1, internal, 44611, 44694
Valid prediction for snap_scaffold_7-snap.1731-T1
Valid prediction for HiQ_model.g11959.t1
Valid prediction for CodingQuarry_transcript_57574-T1
Valid prediction for pasa_asmbl_50059.p1
Valid prediction for GlimmerHMM_glimmerT_17839-T1
Valid prediction for GlimmerHMM_glimmerT_17822-T1
Valid prediction for snap_scaffold_7-snap.1739-T1
Valid prediction for Augustus_model.g11955.t1
Valid prediction for CodingQuarry_transcript_57576-T1
Valid prediction for Augustus_model.g11972.t1
Valid prediction for pasa_asmbl_50043.p1
Valid prediction for GlimmerHMM_glimmerT_17818-T1
Valid prediction for snap_scaffold_7-snap.1727-T1
Valid prediction for pasa_asmbl_50066.p1
Valid prediction for GlimmerHMM_glimmerT_17832-T1
Valid prediction for snap_scaffold_7-snap.1751-T1
Valid prediction for CodingQuarry_transcript_57581-T1
Valid prediction for snap_scaffold_7-snap.1753-T1
Valid prediction for snap_scaffold_7-snap.1742-T1
Valid prediction for Augustus_model.g11961.t1
Valid prediction for CodingQuarry_transcript_57578-T1
Valid prediction for Augustus_model.g11967.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 pasa_asmbl_51039.p1
Valid prediction for snap_scaffold_7-snap.1736-T1
Valid prediction for snap_scaffold_7-snap.1757-T1
Valid prediction for GlimmerHMM_glimmerT_17833-T1
Valid prediction for snap_scaffold_7-snap.1746-T1
Valid prediction for HiQ_model.g11962.t1
Valid prediction for HiQ_model.g11973.t1
Valid prediction for snap_scaffold_7-snap.1740-T1
Valid prediction for pasa_asmbl_51567.p1
Valid prediction for snap_scaffold_7-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_17819-T1
Valid prediction for GlimmerHMM_glimmerT_17834-T1
Valid prediction for Augustus_model.g11958.t1
Valid prediction for GlimmerHMM_glimmerT_17835-T1
Valid prediction for HiQ_model.g11966.t1
Valid prediction for CodingQuarry_transcript_57577-T1
Valid prediction for GlimmerHMM_glimmerT_17820-T1
Valid prediction for GlimmerHMM_glimmerT_17831-T1
Valid prediction for snap_scaffold_7-snap.1755-T1
Valid prediction for snap_scaffold_7-snap.1750-T1
Valid prediction for Augustus_model.g11970.t1
Couldn't classify 29923, 30459
Sorry, prediction pasa_asmbl_51042.p1 fails validation.
(ACT)	 TA	29923-30459	GG	GAG
Valid prediction for Augustus_model.g11964.t1
Valid prediction for Augustus_model.g11978.t1
Valid prediction for CodingQuarry_transcript_57579-T1
Valid prediction for CodingQuarry_transcript_57580-T1
Valid prediction for Augustus_model.g11969.t1
Valid prediction for snap_scaffold_7-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_17837-T1
Valid prediction for GlimmerHMM_glimmerT_17815-T1
Valid prediction for snap_scaffold_7-snap.1754-T1
Valid prediction for snap_scaffold_7-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_17829-T1
Valid prediction for GlimmerHMM_glimmerT_17826-T1
Valid prediction for snap_scaffold_7-snap.1743-T1
Valid prediction for Augustus_model.g11975.t1
Valid prediction for GlimmerHMM_glimmerT_17824-T1
Valid prediction for pasa_asmbl_51038.p1
Valid prediction for snap_scaffold_7-snap.1756-T1
Valid prediction for Augustus_model.g11963.t1
Valid prediction for pasa_asmbl_51037.p1
Valid prediction for GlimmerHMM_glimmerT_17838-T1
Valid prediction for snap_scaffold_7-snap.1744-T1
Valid prediction for Augustus_model.g11976.t1
Valid prediction for snap_scaffold_7-snap.1752-T1
Couldn't classify 191078, 191321
Couldn't classify 191988, 192104
Sorry, prediction pasa_asmbl_51036.p1 fails validation.
(CCC)	 TA	191078-191321	GT	AAG
(ATC)	 AG	191408-191651	GT	AGG
(GGG)	 AG	191766-191898	GT	AGG
(GTG)	 AG	191988-192104	TA	AAT
-recovered pasa_asmbl_51036.p1, internal, 191408, 191651
-recovered pasa_asmbl_51036.p1, internal, 191766, 191898
Valid prediction for snap_scaffold_7-snap.1729-T1
Valid prediction for snap_scaffold_7-snap.1734-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)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 - 215812
-exon list size: 396


building trellis

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1.0    
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11.6    
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18.1    
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18.6    
18.8    
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19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
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62.6    
62.8    
63.1    
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63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
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 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 198552 - 215812
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 198552 - 210725
-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