-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_185363-411963

-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 Augustus_model.g16377.t1
Valid prediction for GlimmerHMM_glimmerT_24469-T1
Valid prediction for snap_scaffold_10-snap.83-T1
Valid prediction for Augustus_model.g16392.t1
Valid prediction for snap_scaffold_10-snap.63-T1
Valid prediction for snap_scaffold_10-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_24450-T1
Valid prediction for snap_scaffold_10-snap.70-T1
Valid prediction for snap_scaffold_10-snap.86-T1
Valid prediction for snap_scaffold_10-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_24464-T1
Valid prediction for GeneMark_model.41838_t
Valid prediction for GeneMark_model.41851_t
Valid prediction for GlimmerHMM_glimmerT_24470-T1
Valid prediction for GlimmerHMM_glimmerT_24446-T1
Valid prediction for GlimmerHMM_glimmerT_24479-T1
Valid prediction for GeneMark_model.41845_t
Valid prediction for GeneMark_model.41824_t
Valid prediction for pasa_asmbl_4139.p1
Valid prediction for GlimmerHMM_glimmerT_24480-T1
Valid prediction for Augustus_model.g16388.t1
Valid prediction for GeneMark_model.41831_t
Valid prediction for GeneMark_model.41849_t
Valid prediction for Augustus_model.g16397.t1
Valid prediction for GeneMark_model.41843_t
Valid prediction for Augustus_model.g16375.t1
Valid prediction for GlimmerHMM_glimmerT_24478-T1
Valid prediction for snap_scaffold_10-snap.68-T1
Valid prediction for snap_scaffold_10-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_24451-T1
Valid prediction for Augustus_model.g16379.t1
Valid prediction for snap_scaffold_10-snap.59-T1
Valid prediction for Augustus_model.g16368.t1
Valid prediction for Augustus_model.g16370.t1
Valid prediction for GeneMark_model.41835_t
Valid prediction for snap_scaffold_10-snap.74-T1
Valid prediction for GeneMark_model.41837_t
Valid prediction for GlimmerHMM_glimmerT_24448-T1
Valid prediction for Augustus_model.g16367.t1
Valid prediction for snap_scaffold_10-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_24457-T1
Valid prediction for Augustus_model.g16398.t1
Valid prediction for snap_scaffold_10-snap.47-T1
Valid prediction for Augustus_model.g16373.t1
Valid prediction for GlimmerHMM_glimmerT_24459-T1
Valid prediction for GlimmerHMM_glimmerT_24467-T1
Valid prediction for GlimmerHMM_glimmerT_24444-T1
Valid prediction for snap_scaffold_10-snap.75-T1
Couldn't classify 17787, 18188
Sorry, prediction pasa_asmbl_2838.p1 fails validation.
(ATG)	 TC	17787-18188	TC	ACT
Valid prediction for GeneMark_model.41850_t
Valid prediction for snap_scaffold_10-snap.46-T1
Valid prediction for Augustus_model.g16383.t1
Valid prediction for GlimmerHMM_glimmerT_24466-T1
Valid prediction for snap_scaffold_10-snap.52-T1
Valid prediction for snap_scaffold_10-snap.60-T1
Valid prediction for GeneMark_model.41839_t
Valid prediction for snap_scaffold_10-snap.56-T1
Valid prediction for Augustus_model.g16376.t1
Valid prediction for GlimmerHMM_glimmerT_24481-T1
Valid prediction for GlimmerHMM_glimmerT_24453-T1
Valid prediction for Augustus_model.g16393.t1
Valid prediction for snap_scaffold_10-snap.76-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_24460-T1
Couldn't classify 67384, 67557
Sorry, prediction pasa_asmbl_2856.p1 fails validation.
(AGT)	 AG	67384-67557	GT	TGG
(ACT)	 AG	68521-68559	GT	AGG
(GAA)	 AG	69784-69948	TG	AGT
-recovered pasa_asmbl_2856.p1, terminal, 69784, 69948
-recovered pasa_asmbl_2856.p1, internal, 67384, 67557
-recovered pasa_asmbl_2856.p1, internal, 68521, 68559
Valid prediction for GlimmerHMM_glimmerT_24474-T1
Valid prediction for Augustus_model.g16384.t1
Valid prediction for CodingQuarry_transcript_5238-T1
Valid prediction for Augustus_model.g16382.t1
Valid prediction for GlimmerHMM_glimmerT_24463-T1
Valid prediction for GlimmerHMM_glimmerT_24447-T1
Valid prediction for Augustus_model.g16387.t1
Valid prediction for snap_scaffold_10-snap.58-T1
Valid prediction for pasa_asmbl_2867.p1
Couldn't classify 97605, 97856
Sorry, prediction pasa_asmbl_2846.p1 fails validation.
(ATG)	 GC	97303-97419	GT	AAG
(GCT)	 AG	97605-97856	AT	CCA
-recovered pasa_asmbl_2846.p1, initial, 97303, 97419
Valid prediction for snap_scaffold_10-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_24461-T1
Valid prediction for snap_scaffold_10-snap.66-T1
Couldn't classify 73931, 74027
Couldn't classify 80393, 80506
Sorry, prediction pasa_asmbl_2850.p1 fails validation.
(CAG)	 TT	73931-74027	GT	GGG
(GAG)	 AG	74165-74271	GC	AGG
(CAT)	 AG	74480-74538	GT	AAG
(TAA)	 AG	74637-74778	GT	AGG
(TTC)	 AG	74881-74970	GT	AGG
(CTG)	 AG	77038-77145	GT	AGG
(GTG)	 AG	77253-77340	GT	ATG
(CGG)	 AG	77665-77801	GT	AAG
(CTA)	 AG	78202-78420	GT	TGG
(ACT)	 AG	80393-80506	GT	AGG
-recovered pasa_asmbl_2850.p1, internal, 74165, 74271
-recovered pasa_asmbl_2850.p1, internal, 74480, 74538
-recovered pasa_asmbl_2850.p1, internal, 74637, 74778
-recovered pasa_asmbl_2850.p1, internal, 74881, 74970
-recovered pasa_asmbl_2850.p1, internal, 77038, 77145
-recovered pasa_asmbl_2850.p1, internal, 77253, 77340
-recovered pasa_asmbl_2850.p1, internal, 77665, 77801
-recovered pasa_asmbl_2850.p1, internal, 78202, 78420
-recovered pasa_asmbl_2850.p1, internal, 80393, 80506
Valid prediction for GlimmerHMM_glimmerT_24456-T1
Valid prediction for snap_scaffold_10-snap.45-T1
Valid prediction for snap_scaffold_10-snap.62-T1
Couldn't classify 206621, 206744
Sorry, prediction pasa_asmbl_2843.p1 fails validation.
(ATG)	 AA	201487-201546	GT	AGG
(GTT)	 AG	202183-202321	GT	CCG
(CTG)	 AG	202463-202581	GT	AGG
(GCA)	 AG	202749-202823	GT	AGG
(GCG)	 AG	203164-203271	GT	AGG
(GTA)	 AG	203537-203615	GT	AGG
(AGA)	 AG	203702-203813	GT	AAG
(TCC)	 AG	203974-204063	GT	AAG
(TTC)	 AG	204152-204324	GT	AGG
(GTG)	 AG	204417-204529	GT	AGG
(TTT)	 AG	204614-204821	GT	TGG
(GGA)	 AG	204955-205044	GT	AGG
(GCG)	 AG	205871-206051	GT	GGG
(GTA)	 AG	206197-206296	GT	ACG
(ACC)	 AG	206394-206545	GT	ATG
(TTC)	 AG	206621-206744	AG	ACA
-recovered pasa_asmbl_2843.p1, initial, 201487, 201546
add_exon() Sorry, pasa_asmbl_2843.p1 204152-204324-terminal-2 is invalid.
-recovered pasa_asmbl_2843.p1, terminal, 204152, 204324
-recovered pasa_asmbl_2843.p1, internal, 202183, 202321
-recovered pasa_asmbl_2843.p1, internal, 202463, 202581
-recovered pasa_asmbl_2843.p1, internal, 202749, 202823
-recovered pasa_asmbl_2843.p1, internal, 203164, 203271
-recovered pasa_asmbl_2843.p1, internal, 203537, 203615
-recovered pasa_asmbl_2843.p1, internal, 203702, 203813
-recovered pasa_asmbl_2843.p1, internal, 203974, 204063
-recovered pasa_asmbl_2843.p1, internal, 204152, 204324
-recovered pasa_asmbl_2843.p1, internal, 204417, 204529
-recovered pasa_asmbl_2843.p1, internal, 204614, 204821
-recovered pasa_asmbl_2843.p1, internal, 204955, 205044
-recovered pasa_asmbl_2843.p1, internal, 205871, 206051
-recovered pasa_asmbl_2843.p1, internal, 206197, 206296
-recovered pasa_asmbl_2843.p1, internal, 206394, 206545
Couldn't classify 83768, 83989
Couldn't classify 85915, 86133
Sorry, prediction pasa_asmbl_2849.p1 fails validation.
(GAC)	 TT	83768-83989	GT	TGG
(GAA)	 AG	85086-85182	GT	AGG
(GAG)	 AG	85346-85437	GT	TGG
(GTG)	 AG	85915-86133	TA	GGT
-recovered pasa_asmbl_2849.p1, internal, 85086, 85182
-recovered pasa_asmbl_2849.p1, internal, 85346, 85437
Valid prediction for GlimmerHMM_glimmerT_24452-T1
Valid prediction for snap_scaffold_10-snap.57-T1
Valid prediction for snap_scaffold_10-snap.79-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g16371.t1
Valid prediction for GlimmerHMM_glimmerT_24445-T1
Valid prediction for GlimmerHMM_glimmerT_24476-T1
Valid prediction for Augustus_model.g16389.t1
Valid prediction for Augustus_model.g16386.t1
Valid prediction for GeneMark_model.41844_t
Valid prediction for Augustus_model.g16391.t1
Valid prediction for snap_scaffold_10-snap.50-T1
Valid prediction for HiQ_model.g16390.t1
Valid prediction for HiQ_model.g16366.t1
Valid prediction for Augustus_model.g16385.t1
Valid prediction for CodingQuarry_transcript_5242-T1
Valid prediction for GlimmerHMM_glimmerT_24455-T1
Valid prediction for snap_scaffold_10-snap.64-T1
Valid prediction for HiQ_model.g16369.t1
Valid prediction for GeneMark_model.41846_t
Valid prediction for snap_scaffold_10-snap.65-T1
Valid prediction for snap_scaffold_10-snap.88-T1
Valid prediction for CodingQuarry_transcript_5241-T1
Valid prediction for HiQ_model.g16396.t1
Valid prediction for snap_scaffold_10-snap.78-T1
Valid prediction for snap_scaffold_10-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_24462-T1
Valid prediction for snap_scaffold_10-snap.69-T1
Couldn't classify 219864, 220106
Sorry, prediction pasa_asmbl_2833.p1 fails validation.
(AGA)	 CT	219864-220106	GT	AGG
(TAC)	 AG	220192-220315	GT	CGG
(ACG)	 AG	220568-220633	GT	AGG
(AAA)	 AG	220732-220829	GT	AGG
(ACT)	 AG	220940-221044	GT	TGG
(CCT)	 AG	221255-221383	GT	AGG
(GAT)	 AG	221470-221592	AA	GAA
-recovered pasa_asmbl_2833.p1, terminal, 221470, 221592
-recovered pasa_asmbl_2833.p1, internal, 220192, 220315
-recovered pasa_asmbl_2833.p1, internal, 220568, 220633
-recovered pasa_asmbl_2833.p1, internal, 220732, 220829
-recovered pasa_asmbl_2833.p1, internal, 220940, 221044
-recovered pasa_asmbl_2833.p1, internal, 221255, 221383
Valid prediction for GeneMark_model.41828_t
Valid prediction for Augustus_model.g16378.t1
Valid prediction for snap_scaffold_10-snap.61-T1
Valid prediction for GlimmerHMM_glimmerT_24477-T1
Valid prediction for snap_scaffold_10-snap.81-T1
Valid prediction for GeneMark_model.41830_t
Valid prediction for Augustus_model.g16372.t1
Valid prediction for Augustus_model.g16380.t1
Valid prediction for snap_scaffold_10-snap.82-T1
Valid prediction for CodingQuarry_transcript_5237-T1
Valid prediction for snap_scaffold_10-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_24473-T1
Valid prediction for Augustus_model.g16381.t1
Valid prediction for Augustus_model.g16395.t1
Valid prediction for snap_scaffold_10-snap.80-T1
Couldn't classify 206621, 206744
Sorry, prediction pasa_asmbl_2842.p1 fails validation.
(ATG)	 GA	203068-203271	GT	AGG
(GTA)	 AG	203537-203615	GT	AGG
(AGA)	 AG	203702-203813	GT	AAG
(TCC)	 AG	203974-204063	GT	AAG
(TTC)	 AG	204152-204324	GT	AGG
(GTG)	 AG	204417-204529	GT	AGG
(TTT)	 AG	204614-204821	GT	TGG
(GGA)	 AG	204955-205044	GT	AGG
(GCG)	 AG	205871-206051	GT	GGG
(GTA)	 AG	206197-206296	GT	ACG
(ACC)	 AG	206394-206545	GT	ATG
(TTC)	 AG	206621-206744	AG	ACA
-recovered pasa_asmbl_2842.p1, initial, 203068, 203271
add_exon() Sorry, pasa_asmbl_2842.p1 204152-204324-terminal-2 is invalid.
-recovered pasa_asmbl_2842.p1, terminal, 204152, 204324
-recovered pasa_asmbl_2842.p1, internal, 203537, 203615
-recovered pasa_asmbl_2842.p1, internal, 203702, 203813
-recovered pasa_asmbl_2842.p1, internal, 203974, 204063
-recovered pasa_asmbl_2842.p1, internal, 204152, 204324
-recovered pasa_asmbl_2842.p1, internal, 204417, 204529
-recovered pasa_asmbl_2842.p1, internal, 204614, 204821
-recovered pasa_asmbl_2842.p1, internal, 204955, 205044
-recovered pasa_asmbl_2842.p1, internal, 205871, 206051
-recovered pasa_asmbl_2842.p1, internal, 206197, 206296
-recovered pasa_asmbl_2842.p1, internal, 206394, 206545
Valid prediction for GeneMark_model.41834_t
Valid prediction for GlimmerHMM_glimmerT_24482-T1
Valid prediction for snap_scaffold_10-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_24472-T1
Valid prediction for GlimmerHMM_glimmerT_24449-T1
Valid prediction for GlimmerHMM_glimmerT_24465-T1
Valid prediction for GlimmerHMM_glimmerT_24443-T1
Valid prediction for GlimmerHMM_glimmerT_24471-T1
Valid prediction for GeneMark_model.41847_t
Valid prediction for GlimmerHMM_glimmerT_24454-T1
Valid prediction for snap_scaffold_10-snap.67-T1
Valid prediction for GeneMark_model.41852_t
Valid prediction for snap_scaffold_10-snap.71-T1
Valid prediction for snap_scaffold_10-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_24458-T1
Valid prediction for GeneMark_model.41825_t
Valid prediction for GeneMark_model.41836_t
Valid prediction for GeneMark_model.41840_t
Valid prediction for snap_scaffold_10-snap.54-T1
Valid prediction for Augustus_model.g16374.t1
Valid prediction for GeneMark_model.41848_t
Valid prediction for snap_scaffold_10-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_24468-T1
Valid prediction for GlimmerHMM_glimmerT_24475-T1
Valid prediction for CodingQuarry_transcript_5240-T1
Valid prediction for Augustus_model.g16394.t1
Couldn't classify 100908, 101210
Sorry, prediction pasa_asmbl_2845.p1 fails validation.
(GGA)	 CT	100908-101210	GT	AAG
Valid prediction for snap_scaffold_10-snap.51-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 226601
-exon list size: 484


building trellis

0.2    
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1.0    
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1.4    
1.6    
1.9    
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2.7    
2.9    
3.1    
3.3    
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3.7    
3.9    
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4.3    
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5.6    
5.8    
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6.8    
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11.3    
11.5    
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13.6    
13.8    
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14.2    
14.4    
14.6    
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16.9    
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17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
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19.3    
19.5    
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20.0    
20.2    
20.4    
20.6    
20.8    
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21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
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23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
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24.9    
25.1    
25.3    
25.5    
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25.9    
26.1    
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26.5    
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27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
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    
84.0    
84.2    
84.4    
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    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 46 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support