-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_1-163668

-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.g15909.t1
Valid prediction for GlimmerHMM_glimmerT_23905-T1
Couldn't classify 1199, 1378
Sorry, prediction pasa_asmbl_2841.p1 fails validation.
(AGG)	 TC	1199-1378	GT	AGG
(TGT)	 AG	2280-2486	GT	AGG
(GGT)	 AG	2901-3083	GT	AGG
(GAG)	 AG	4575-4658	GT	AGG
(CCT)	 AG	4887-4919	CA	AAC
-recovered pasa_asmbl_2841.p1, terminal, 4887, 4919
-recovered pasa_asmbl_2841.p1, internal, 2280, 2486
-recovered pasa_asmbl_2841.p1, internal, 2901, 3083
-recovered pasa_asmbl_2841.p1, internal, 4575, 4658
Valid prediction for Augustus_model.g15902.t1
Valid prediction for Augustus_model.g15900.t1
Couldn't classify 147193, 147335
Couldn't classify 155243, 155400
Sorry, prediction pasa_asmbl_2842.p1 fails validation.
(AGT)	 CC	147193-147335	GT	AGG
(CCG)	 AG	150179-150319	GT	AGG
(TGA)	 AG	152210-152310	GT	GGG
(GCG)	 AG	155243-155400	AG	AGA
-recovered pasa_asmbl_2842.p1, internal, 150179, 150319
-recovered pasa_asmbl_2842.p1, internal, 152210, 152310
Valid prediction for snap_scaffold_10-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_23907-T1
Valid prediction for GlimmerHMM_glimmerT_23880-T1
Valid prediction for GlimmerHMM_glimmerT_23902-T1
Valid prediction for snap_scaffold_10-snap.16-T1
Valid prediction for snap_scaffold_10-snap.38-T1
Valid prediction for snap_scaffold_10-snap.2-T1
Valid prediction for snap_scaffold_10-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_23885-T1
Valid prediction for GlimmerHMM_glimmerT_23900-T1
Valid prediction for Augustus_model.g15912.t1
Valid prediction for Augustus_model.g15906.t1
Valid prediction for GlimmerHMM_glimmerT_23883-T1
Valid prediction for snap_scaffold_10-snap.8-T1
Valid prediction for CodingQuarry_transcript_5239-T1
Valid prediction for GlimmerHMM_glimmerT_23906-T1
Valid prediction for snap_scaffold_10-snap.35-T1
Valid prediction for snap_scaffold_10-snap.28-T1
Valid prediction for snap_scaffold_10-snap.36-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.7-T1
Valid prediction for snap_scaffold_10-snap.4-T1
Valid prediction for snap_scaffold_10-snap.15-T1
Valid prediction for snap_scaffold_10-snap.21-T1
Valid prediction for snap_scaffold_10-snap.17-T1
Valid prediction for CodingQuarry_transcript_5240-T1
Valid prediction for snap_scaffold_10-snap.18-T1
Valid prediction for Augustus_model.g15891.t1
Valid prediction for Augustus_model.g15893.t1
Valid prediction for snap_scaffold_10-snap.1-T1
Couldn't classify 1213, 1378
Sorry, prediction Augustus_model.g15889.t1 fails validation.
(GTT)	 AG	1213-1378	GT	AGG
(TGT)	 AG	2280-2486	GT	AGG
(GGT)	 AG	2901-3083	GT	AGG
(GAG)	 AG	4575-4658	GT	AGG
(CCT)	 AG	4887-4919	CA	AAC
-recovered Augustus_model.g15889.t1, terminal, 4887, 4919
-recovered Augustus_model.g15889.t1, internal, 1213, 1378
-recovered Augustus_model.g15889.t1, internal, 2280, 2486
-recovered Augustus_model.g15889.t1, internal, 2901, 3083
-recovered Augustus_model.g15889.t1, internal, 4575, 4658
Valid prediction for GlimmerHMM_glimmerT_23882-T1
Valid prediction for Augustus_model.g15914.t1
Valid prediction for snap_scaffold_10-snap.30-T1
Valid prediction for Augustus_model.g15907.t1
Valid prediction for GlimmerHMM_glimmerT_23893-T1
Valid prediction for GlimmerHMM_glimmerT_23897-T1
Valid prediction for Augustus_model.g15913.t1
Valid prediction for Augustus_model.g15899.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_23895-T1
Valid prediction for Augustus_model.g15903.t1
Valid prediction for snap_scaffold_10-snap.11-T1
Valid prediction for Augustus_model.g15896.t1
Valid prediction for Augustus_model.g15890.t1
Valid prediction for GlimmerHMM_glimmerT_23904-T1
Couldn't classify 127443, 127452
Couldn't classify 131333, 131452
Sorry, prediction pasa_asmbl_3911.p1 fails validation.
(TCT)	 CC	127443-127452	GT	TGG
(GTG)	 AG	127701-127797	GT	AGG
(GTA)	 AG	129538-129625	GT	TAG
(ATT)	 AG	129769-129849	GT	AGG
(AAG)	 AG	129940-130022	GT	AGG
(AGC)	 AG	131099-131204	GT	AGG
(GAG)	 AG	131333-131452	GT	AGG
-recovered pasa_asmbl_3911.p1, internal, 127701, 127797
-recovered pasa_asmbl_3911.p1, internal, 129538, 129625
-recovered pasa_asmbl_3911.p1, internal, 129769, 129849
-recovered pasa_asmbl_3911.p1, internal, 129940, 130022
-recovered pasa_asmbl_3911.p1, internal, 131099, 131204
-recovered pasa_asmbl_3911.p1, internal, 131333, 131452
Valid prediction for snap_scaffold_10-snap.29-T1
Valid prediction for Augustus_model.g15915.t1
Valid prediction for snap_scaffold_10-snap.14-T1
Valid prediction for snap_scaffold_10-snap.39-T1
Valid prediction for snap_scaffold_10-snap.22-T1
Valid prediction for Augustus_model.g15897.t1
Valid prediction for snap_scaffold_10-snap.33-T1
Valid prediction for Augustus_model.g15910.t1
Valid prediction for GlimmerHMM_glimmerT_23892-T1
Couldn't classify 117520, 117597
Couldn't classify 118691, 118703
Sorry, prediction pasa_asmbl_3913.p1 fails validation.
(CAC)	 TG	117520-117597	GT	TTG
(AGT)	 AG	118067-118235	GT	TGG
(AAA)	 AG	118318-118408	GT	GGG
(GAA)	 AG	118691-118703	AG	GCA
-recovered pasa_asmbl_3913.p1, internal, 118067, 118235
-recovered pasa_asmbl_3913.p1, internal, 118318, 118408
Valid prediction for GlimmerHMM_glimmerT_23888-T1
Valid prediction for Augustus_model.g15911.t1
Valid prediction for GlimmerHMM_glimmerT_23903-T1
Valid prediction for snap_scaffold_10-snap.27-T1
Valid prediction for snap_scaffold_10-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_23889-T1
Valid prediction for GlimmerHMM_glimmerT_23896-T1
Valid prediction for Augustus_model.g15892.t1
Valid prediction for GlimmerHMM_glimmerT_23901-T1
Valid prediction for snap_scaffold_10-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_23908-T1
Valid prediction for snap_scaffold_10-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_23898-T1
Couldn't classify 126753, 126769
Sorry, prediction pasa_asmbl_3912.p1 fails validation.
(ATG)	 AA	125947-126180	GT	ATG
(AAT)	 AG	126455-126590	GT	TGG
(TGG)	 AG	126753-126769	GA	GCG
-recovered pasa_asmbl_3912.p1, initial, 125947, 126180
-recovered pasa_asmbl_3912.p1, internal, 126455, 126590
Valid prediction for snap_scaffold_10-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_23886-T1
Valid prediction for Augustus_model.g15904.t1
Valid prediction for snap_scaffold_10-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_23899-T1
Valid prediction for GlimmerHMM_glimmerT_23890-T1
Valid prediction for snap_scaffold_10-snap.32-T1
Valid prediction for snap_scaffold_10-snap.6-T1
Valid prediction for Augustus_model.g15905.t1
Valid prediction for Augustus_model.g15894.t1
Valid prediction for snap_scaffold_10-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_23881-T1
Couldn't classify 119004, 119207
Couldn't classify 119575, 119742
Sorry, prediction pasa_asmbl_5198.p1 fails validation.
(GAG)	 CA	119004-119207	GT	AGG
(ATT)	 AG	119575-119742	TA	GGT
Couldn't classify 147837, 147959
Sorry, prediction pasa_asmbl_3908.p1 fails validation.
(ATG)	 GG	144455-144568	GT	AGG
(ATT)	 AG	146994-147189	GT	AGG
(ACG)	 AG	147432-147538	GT	AGG
(GTG)	 AG	147837-147959	GG	TGG
-recovered pasa_asmbl_3908.p1, initial, 144455, 144568
-recovered pasa_asmbl_3908.p1, internal, 146994, 147189
-recovered pasa_asmbl_3908.p1, internal, 147432, 147538
Valid prediction for snap_scaffold_10-snap.31-T1
Valid prediction for snap_scaffold_10-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_23887-T1
Valid prediction for snap_scaffold_10-snap.20-T1
Valid prediction for Augustus_model.g15901.t1
Valid prediction for Augustus_model.g15898.t1
Valid prediction for Augustus_model.g15908.t1
Couldn't classify 138044, 138316
Couldn't classify 138449, 138538
Sorry, prediction pasa_asmbl_3910.p1 fails validation.
(ACC)	 AG	138044-138316	GT	AGG
(GCA)	 AG	138449-138538	AT	GGA
-recovered pasa_asmbl_3910.p1, internal, 138044, 138316
Valid prediction for snap_scaffold_10-snap.5-T1
Valid prediction for snap_scaffold_10-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_23891-T1
Valid prediction for snap_scaffold_10-snap.19-T1
Valid prediction for Augustus_model.g15895.t1
Valid prediction for GlimmerHMM_glimmerT_23884-T1
Valid prediction for GlimmerHMM_glimmerT_23894-T1
Valid prediction for snap_scaffold_10-snap.37-T1

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

-building trellis in range 1 - 163668
-exon list size: 261


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.0    
3.4    
3.8    
4.2    
4.6    
4.9    
5.3    
5.7    
6.1    
6.5    
6.8    
7.2    
7.6    
8.0    
8.4    
8.7    
9.1    
9.5    
9.9    
10.3    
10.6    
11.0    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.1    
14.4    
14.8    
15.2    
15.6    
16.0    
16.3    
16.7    
17.1    
17.5    
17.9    
18.3    
18.6    
19.0    
19.4    
19.8    
20.2    
20.5    
20.9    
21.3    
21.7    
22.1    
22.4    
22.8    
23.2    
23.6    
24.0    
24.3    
24.7    
25.1    
25.5    
25.9    
26.2    
26.6    
27.0    
27.4    
27.8    
28.1    
28.5    
28.9    
29.3    
29.7    
30.0    
30.4    
30.8    
31.2    
31.6    
31.9    
32.3    
32.7    
33.1    
33.5    
33.8    
34.2    
34.6    
35.0    
35.4    
35.7    
36.1    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.8    
39.2    
39.5    
39.9    
40.3    
40.7    
41.1    
41.4    
41.8    
42.2    
42.6    
43.0    
43.3    
43.7    
44.1    
44.5    
44.9    
45.2    
45.6    
46.0    
46.4    
46.8    
47.1    
47.5    
47.9    
48.3    
48.7    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.3    
51.7    
52.1    
52.5    
52.9    
53.2    
53.6    
54.0    
54.4    
54.8    
55.1    
55.5    
55.9    
56.3    
56.7    
57.0    
57.4    
57.8    
58.2    
58.6    
58.9    
59.3    
59.7    
60.1    
60.5    
60.8    
61.2    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.9    
64.3    
64.6    
65.0    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.7    
68.1    
68.4    
68.8    
69.2    
69.6    
70.0    
70.3    
70.7    
71.1    
71.5    
71.9    
72.2    
72.6    
73.0    
73.4    
73.8    
74.1    
74.5    
74.9    
75.3    
75.7    
76.0    
76.4    
76.8    
77.2    
77.6    
77.9    
78.3    
78.7    
79.1    
79.5    
79.8    
80.2    
80.6    
81.0    
81.4    
81.7    
82.1    
82.5    
82.9    
83.3    
83.7    
84.0    
84.4    
84.8    
85.2    
85.6    
85.9    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
89.0    
89.4    
89.7    
90.1    
90.5    
90.9    
91.3    
91.6    
92.0    
92.4    
92.8    
93.2    
93.5    
93.9    
94.3    
94.7    
95.1    
95.4    
95.8    
96.2    
96.6    
97.0    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 32 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support