-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_16250446-16460657

-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 CodingQuarry_transcript_10518-T1
Valid prediction for Augustus_model.g20421.t1
Valid prediction for CodingQuarry_transcript_10520-T1
Valid prediction for GlimmerHMM_glimmerT_30810-T1
Valid prediction for pasa_asmbl_8165.p1
Valid prediction for CodingQuarry_transcript_10517-T1
Valid prediction for snap_scaffold_12-snap.3155-T1
Valid prediction for HiQ_model.g20404.t1
Valid prediction for GlimmerHMM_glimmerT_30793-T1
Valid prediction for GlimmerHMM_glimmerT_30800-T1
Valid prediction for snap_scaffold_12-snap.3120-T1
Valid prediction for snap_scaffold_12-snap.3118-T1
Valid prediction for Augustus_model.g20397.t1
Valid prediction for GlimmerHMM_glimmerT_30792-T1
Valid prediction for snap_scaffold_12-snap.3130-T1
Valid prediction for snap_scaffold_12-snap.3135-T1
Valid prediction for CodingQuarry_transcript_10522-T1
Valid prediction for GlimmerHMM_glimmerT_30812-T1
Couldn't classify 101397, 101538
Couldn't classify 102063, 102162
Sorry, prediction pasa_asmbl_8200.p1 fails validation.
(AGG)	 GC	101397-101538	GT	AGG
(CAC)	 AG	101696-101849	GT	GTG
(TTT)	 AG	102063-102162	GG	AAG
-recovered pasa_asmbl_8200.p1, internal, 101696, 101849
Valid prediction for Augustus_model.g20391.t1
Valid prediction for Augustus_model.g20395.t1
Valid prediction for GlimmerHMM_glimmerT_30788-T1
Valid prediction for GlimmerHMM_glimmerT_30813-T1
Valid prediction for Augustus_model.g20408.t1
Valid prediction for snap_scaffold_12-snap.3143-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 162331, 162543
Couldn't classify 165096, 165275
Sorry, prediction pasa_asmbl_8179.p1 fails validation.
(TTT)	 GT	162331-162543	GT	ATG
(GTG)	 AG	163670-163810	GT	AGG
(GTT)	 AG	164023-164123	GT	AGG
(AAT)	 AG	164625-164778	GT	AGG
(GAC)	 AG	164892-164993	GT	AGG
(ATT)	 AG	165096-165275	GT	AGG
add_exon() Sorry, pasa_asmbl_8179.p1 164023-164123-terminal-2 is invalid.
-recovered pasa_asmbl_8179.p1, terminal, 164023, 164123
-recovered pasa_asmbl_8179.p1, internal, 163670, 163810
-recovered pasa_asmbl_8179.p1, internal, 164023, 164123
-recovered pasa_asmbl_8179.p1, internal, 164625, 164778
-recovered pasa_asmbl_8179.p1, internal, 164892, 164993
-recovered pasa_asmbl_8179.p1, internal, 165096, 165275
Couldn't classify 106735, 106844
Couldn't classify 106961, 107159
Sorry, prediction pasa_asmbl_8206.p1 fails validation.
(GGA)	 TA	106735-106844	GT	AGG
(GGG)	 AG	106961-107159	GC	AGG
-recovered pasa_asmbl_8206.p1, internal, 106961, 107159
Valid prediction for Augustus_model.g20407.t1
Valid prediction for snap_scaffold_12-snap.3144-T1
Valid prediction for Augustus_model.g20419.t1
Valid prediction for GlimmerHMM_glimmerT_30807-T1
Valid prediction for Augustus_model.g20394.t1
Valid prediction for snap_scaffold_12-snap.3154-T1
Valid prediction for snap_scaffold_12-snap.3150-T1
Valid prediction for Augustus_model.g20412.t1
Valid prediction for Augustus_model.g20399.t1
Valid prediction for Augustus_model.g20420.t1
Valid prediction for pasa_asmbl_8188.p1
Valid prediction for snap_scaffold_12-snap.3149-T1
Valid prediction for snap_scaffold_12-snap.3151-T1
Valid prediction for snap_scaffold_12-snap.3131-T1
Valid prediction for Augustus_model.g20411.t1
Couldn't classify 78161, 78186
Couldn't classify 78667, 80701
Sorry, prediction pasa_asmbl_8160.p1 fails validation.
(ACA)	 AC	78161-78186	GT	AGG
(GTG)	 AG	78667-80701	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_30806-T1
Valid prediction for snap_scaffold_12-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_30804-T1
Valid prediction for GlimmerHMM_glimmerT_30811-T1
Valid prediction for snap_scaffold_12-snap.3145-T1
Valid prediction for GlimmerHMM_glimmerT_30808-T1
Valid prediction for pasa_asmbl_8171.p1
Valid prediction for Augustus_model.g20406.t1
Valid prediction for Augustus_model.g20403.t1
Couldn't classify 92712, 92889
Couldn't classify 96345, 96440
Sorry, prediction pasa_asmbl_8164.p1 fails validation.
(GTG)	 AG	92712-92889	GT	AGG
(GTC)	 AG	93720-93857	GT	GTG
(ACC)	 AG	94789-94964	GT	AGG
(AGA)	 AG	95688-95805	GT	TGG
(GTG)	 AG	96070-96200	GT	AGG
(GGA)	 AG	96345-96440	TA	GGT
-recovered pasa_asmbl_8164.p1, internal, 92712, 92889
-recovered pasa_asmbl_8164.p1, internal, 93720, 93857
-recovered pasa_asmbl_8164.p1, internal, 94789, 94964
-recovered pasa_asmbl_8164.p1, internal, 95688, 95805
-recovered pasa_asmbl_8164.p1, internal, 96070, 96200
Valid prediction for HiQ_model.g20413.t1
Valid prediction for snap_scaffold_12-snap.3141-T1
Valid prediction for CodingQuarry_transcript_10519-T1
Valid prediction for GlimmerHMM_glimmerT_30799-T1
Valid prediction for GlimmerHMM_glimmerT_30797-T1
Valid prediction for Augustus_model.g20417.t1
Valid prediction for GlimmerHMM_glimmerT_30795-T1
Couldn't classify 89269, 89415
Sorry, prediction pasa_asmbl_8161.p1 fails validation.
(ATG)	 AA	83800-83840	GT	CGG
(GAT)	 AG	84875-85008	GT	AGG
(AAG)	 AG	85151-85327	GT	AGG
(TGG)	 AG	87475-87592	GT	AGG
(ATC)	 AG	87876-87975	GT	AGG
(AGT)	 AG	88301-88513	GT	AGG
(ACT)	 AG	88659-88800	GT	CGG
(GAG)	 AG	88929-89038	GT	AGG
(GTT)	 AG	89269-89415	GT	AGG
-recovered pasa_asmbl_8161.p1, initial, 83800, 83840
-recovered pasa_asmbl_8161.p1, internal, 84875, 85008
-recovered pasa_asmbl_8161.p1, internal, 85151, 85327
-recovered pasa_asmbl_8161.p1, internal, 87475, 87592
-recovered pasa_asmbl_8161.p1, internal, 87876, 87975
-recovered pasa_asmbl_8161.p1, internal, 88301, 88513
-recovered pasa_asmbl_8161.p1, internal, 88659, 88800
-recovered pasa_asmbl_8161.p1, internal, 88929, 89038
-recovered pasa_asmbl_8161.p1, internal, 89269, 89415
Valid prediction for Augustus_model.g20389.t1
Valid prediction for GlimmerHMM_glimmerT_30801-T1
Valid prediction for Augustus_model.g20388.t1
Valid prediction for snap_scaffold_12-snap.3134-T1
Valid prediction for Augustus_model.g20393.t1
Valid prediction for Augustus_model.g20401.t1
Valid prediction for Augustus_model.g20402.t1
Valid prediction for Augustus_model.g20409.t1
Valid prediction for snap_scaffold_12-snap.3153-T1
Valid prediction for Augustus_model.g20415.t1
Valid prediction for snap_scaffold_12-snap.3127-T1
Valid prediction for snap_scaffold_12-snap.3133-T1
Valid prediction for snap_scaffold_12-snap.3140-T1
Valid prediction for Augustus_model.g20416.t1
Valid prediction for snap_scaffold_12-snap.3146-T1
Valid prediction for snap_scaffold_12-snap.3132-T1
Valid prediction for CodingQuarry_transcript_10521-T1
Valid prediction for GlimmerHMM_glimmerT_30790-T1
Valid prediction for snap_scaffold_12-snap.3119-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 Augustus_model.g20414.t1
Valid prediction for snap_scaffold_12-snap.3142-T1
Valid prediction for Augustus_model.g20410.t1
Valid prediction for GlimmerHMM_glimmerT_30794-T1
Valid prediction for snap_scaffold_12-snap.3152-T1
Valid prediction for Augustus_model.g20400.t1
Valid prediction for Augustus_model.g20387.t1
Valid prediction for GlimmerHMM_glimmerT_30805-T1
Valid prediction for snap_scaffold_12-snap.3128-T1
Valid prediction for snap_scaffold_12-snap.3139-T1
Couldn't classify 186343, 186475
Sorry, prediction pasa_asmbl_9114.p1 fails validation.
(GGG)	 AG	186343-186475	GT	GGG
(AGG)	 AG	186635-186761	GT	AGG
(CCA)	 AG	186999-187114	GT	AGG
(ATC)	 AG	187286-187323	AG	AAA
-recovered pasa_asmbl_9114.p1, terminal, 186999, 187114
-recovered pasa_asmbl_9114.p1, terminal, 187286, 187323
-recovered pasa_asmbl_9114.p1, internal, 186343, 186475
-recovered pasa_asmbl_9114.p1, internal, 186635, 186761
-recovered pasa_asmbl_9114.p1, internal, 186999, 187114
Valid prediction for snap_scaffold_12-snap.3126-T1
Valid prediction for snap_scaffold_12-snap.3137-T1
Valid prediction for snap_scaffold_12-snap.3148-T1
Valid prediction for Augustus_model.g20418.t1
Valid prediction for GlimmerHMM_glimmerT_30802-T1
Valid prediction for Augustus_model.g20405.t1
Valid prediction for snap_scaffold_12-snap.3129-T1
Valid prediction for GlimmerHMM_glimmerT_30789-T1
Valid prediction for CodingQuarry_transcript_10515-T1
Valid prediction for snap_scaffold_12-snap.3136-T1
Valid prediction for CodingQuarry_transcript_10516-T1
Valid prediction for GlimmerHMM_glimmerT_30791-T1
Valid prediction for GlimmerHMM_glimmerT_30798-T1
Valid prediction for snap_scaffold_12-snap.3121-T1
Valid prediction for Augustus_model.g20398.t1
Valid prediction for snap_scaffold_12-snap.3147-T1
Valid prediction for GlimmerHMM_glimmerT_30809-T1
Valid prediction for snap_scaffold_12-snap.3125-T1
Valid prediction for snap_scaffold_12-snap.3156-T1
Valid prediction for snap_scaffold_12-snap.3117-T1
Valid prediction for snap_scaffold_12-snap.3138-T1
Couldn't classify 149039, 149171
Sorry, prediction pasa_asmbl_9115.p1 fails validation.
(AGA)	 CT	149039-149171	GT	GTG
(TTA)	 AG	149651-149677	GT	AGG
(TGG)	 AG	149815-149909	GT	AGG
(TTC)	 AG	150047-150175	AC	AAA
-recovered pasa_asmbl_9115.p1, terminal, 150047, 150175
-recovered pasa_asmbl_9115.p1, internal, 149651, 149677
-recovered pasa_asmbl_9115.p1, internal, 149815, 149909
Valid prediction for GlimmerHMM_glimmerT_30803-T1
Valid prediction for snap_scaffold_12-snap.3123-T1
Valid prediction for Augustus_model.g20396.t1
Valid prediction for Augustus_model.g20392.t1
Valid prediction for HiQ_model.g20390.t1
Valid prediction for GlimmerHMM_glimmerT_30787-T1
Valid prediction for snap_scaffold_12-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_30796-T1

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

-building trellis in range 1 - 210212
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 42 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support