-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_14082357-14331408

-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.g5076.t1
Valid prediction for snap_scaffold_3-snap.2695-T1
Valid prediction for Augustus_model.g5074.t1
Valid prediction for GlimmerHMM_glimmerT_7703-T1
Valid prediction for snap_scaffold_3-snap.2702-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7701-T1
Valid prediction for snap_scaffold_3-snap.2717-T1
Valid prediction for snap_scaffold_3-snap.2721-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g5061.t1
Valid prediction for GlimmerHMM_glimmerT_7700-T1
Valid prediction for GlimmerHMM_glimmerT_7726-T1
Valid prediction for snap_scaffold_3-snap.2720-T1
Valid prediction for Augustus_model.g5062.t1
Valid prediction for snap_scaffold_3-snap.2730-T1
Valid prediction for Augustus_model.g5089.t1
Valid prediction for GlimmerHMM_glimmerT_7731-T1
Valid prediction for GlimmerHMM_glimmerT_7720-T1
Valid prediction for snap_scaffold_3-snap.2699-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7698-T1
Valid prediction for Augustus_model.g5080.t1
Valid prediction for Augustus_model.g5087.t1
Valid prediction for GlimmerHMM_glimmerT_7697-T1
Couldn't classify 144052, 145908
Sorry, prediction pasa_asmbl_40501.p1 fails validation.
(ATG)	 AA	144052-145908	CT	GGC
Valid prediction for snap_scaffold_3-snap.2726-T1
Valid prediction for Augustus_model.g5067.t1
Valid prediction for Augustus_model.g5092.t1
Couldn't classify 165188, 165508
Sorry, prediction pasa_asmbl_40502.p1 fails validation.
(ATG)	 TC	165188-165508	TA	GGT
Valid prediction for GlimmerHMM_glimmerT_7727-T1
Valid prediction for CodingQuarry_transcript_46343-T1
Valid prediction for snap_scaffold_3-snap.2713-T1
Valid prediction for Augustus_model.g5082.t1
Valid prediction for GlimmerHMM_glimmerT_7705-T1
Valid prediction for snap_scaffold_3-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_7695-T1
Valid prediction for GlimmerHMM_glimmerT_7724-T1
Valid prediction for GlimmerHMM_glimmerT_7694-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_7722-T1
Valid prediction for snap_scaffold_3-snap.2700-T1
Valid prediction for snap_scaffold_3-snap.2712-T1
Valid prediction for GlimmerHMM_glimmerT_7730-T1
Valid prediction for Augustus_model.g5069.t1
Valid prediction for Augustus_model.g5084.t1
Valid prediction for Augustus_model.g5059.t1
Valid prediction for GlimmerHMM_glimmerT_7712-T1
Valid prediction for snap_scaffold_3-snap.2696-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7716-T1
Valid prediction for Augustus_model.g5060.t1
Couldn't classify 174375, 174513
Sorry, prediction pasa_asmbl_40504.p1 fails validation.
(TAT)	 GG	174375-174513	GT	CGG
(CAA)	 AG	174793-174987	GT	AGG
(GAA)	 AG	176899-176962	GT	ATG
(AAC)	 AG	177054-177226	GT	AAG
(ACC)	 AG	177522-177639	GT	AGG
(ACT)	 AG	177890-178142	GA	AAG
-recovered pasa_asmbl_40504.p1, terminal, 177890, 178142
-recovered pasa_asmbl_40504.p1, internal, 174793, 174987
-recovered pasa_asmbl_40504.p1, internal, 176899, 176962
-recovered pasa_asmbl_40504.p1, internal, 177054, 177226
-recovered pasa_asmbl_40504.p1, internal, 177522, 177639
Valid prediction for Augustus_model.g5066.t1
Valid prediction for snap_scaffold_3-snap.2725-T1
Valid prediction for Augustus_model.g5077.t1
Valid prediction for GlimmerHMM_glimmerT_7715-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: -)Couldn't classify 11268, 11413
Couldn't classify 14228, 14294
Sorry, prediction pasa_asmbl_39355.p1 fails validation.
(TTG)	 CT	11268-11413	GT	GGG
(TAT)	 AG	11511-11755	GT	AAG
(TGC)	 AG	11970-12199	GC	AGG
(GAA)	 AG	12281-12381	GT	AAG
(TGA)	 AG	12907-13038	GT	AGG
(GAG)	 AG	13262-13375	GT	CAG
(GTT)	 AG	13593-13745	GC	AGG
(GTG)	 AG	13864-14061	GT	AGG
(ATT)	 AG	14228-14294	AA	TGA
-recovered pasa_asmbl_39355.p1, internal, 11511, 11755
-recovered pasa_asmbl_39355.p1, internal, 11970, 12199
-recovered pasa_asmbl_39355.p1, internal, 12281, 12381
-recovered pasa_asmbl_39355.p1, internal, 12907, 13038
-recovered pasa_asmbl_39355.p1, internal, 13262, 13375
-recovered pasa_asmbl_39355.p1, internal, 13593, 13745
-recovered pasa_asmbl_39355.p1, internal, 13864, 14061
Valid prediction for snap_scaffold_3-snap.2711-T1
Valid prediction for Augustus_model.g5091.t1
Valid prediction for snap_scaffold_3-snap.2714-T1
Couldn't classify 21155, 21544
Sorry, prediction pasa_asmbl_39354.p1 fails validation.
(ATG)	 TT	19234-19326	GT	AGG
(GTG)	 AG	21155-21544	GG	CAG
-recovered pasa_asmbl_39354.p1, initial, 19234, 19326
Valid prediction for snap_scaffold_3-snap.2709-T1
Valid prediction for GlimmerHMM_glimmerT_7732-T1
Valid prediction for snap_scaffold_3-snap.2727-T1
Valid prediction for Augustus_model.g5081.t1
Valid prediction for HiQ_model.g5085.t1
Valid prediction for snap_scaffold_3-snap.2723-T1
Valid prediction for GlimmerHMM_glimmerT_7713-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 59675, 59781
Sorry, prediction pasa_asmbl_39343.p1 fails validation.
(GGA)	 CA	59675-59781	GT	TGG
(GTC)	 AG	59994-60059	GT	GGG
(GTC)	 AG	62562-62642	GT	GGG
(TGG)	 AG	62781-62951	GT	AGG
(GCA)	 AG	65007-65085	GT	AAG
(GAG)	 AG	65204-65350	AA	GAA
-recovered pasa_asmbl_39343.p1, terminal, 65204, 65350
-recovered pasa_asmbl_39343.p1, internal, 59994, 60059
-recovered pasa_asmbl_39343.p1, internal, 62562, 62642
-recovered pasa_asmbl_39343.p1, internal, 62781, 62951
-recovered pasa_asmbl_39343.p1, internal, 65007, 65085
Valid prediction for HiQ_model.g5093.t1
Valid prediction for GlimmerHMM_glimmerT_7704-T1
Valid prediction for Augustus_model.g5094.t1
Valid prediction for snap_scaffold_3-snap.2716-T1
Couldn't classify 28788, 28918
Sorry, prediction pasa_asmbl_39346.p1 fails validation.
(GAT)	 CA	28788-28918	GT	TGG
(TGA)	 AG	29054-29242	GT	AGG
(CTG)	 AG	29432-29585	GT	AGG
(GGG)	 AG	29763-29918	TG	GAT
-recovered pasa_asmbl_39346.p1, terminal, 29763, 29918
-recovered pasa_asmbl_39346.p1, internal, 29054, 29242
-recovered pasa_asmbl_39346.p1, internal, 29432, 29585
Valid prediction for Augustus_model.g5072.t1
Valid prediction for GlimmerHMM_glimmerT_7692-T1
Valid prediction for snap_scaffold_3-snap.2715-T1
Valid prediction for Augustus_model.g5079.t1
Valid prediction for snap_scaffold_3-snap.2708-T1
Valid prediction for GlimmerHMM_glimmerT_7729-T1
Valid prediction for snap_scaffold_3-snap.2733-T1
Valid prediction for GlimmerHMM_glimmerT_7707-T1
Valid prediction for GlimmerHMM_glimmerT_7717-T1
Valid prediction for Augustus_model.g5071.t1
Valid prediction for snap_scaffold_3-snap.2718-T1
Valid prediction for snap_scaffold_3-snap.2706-T1
Valid prediction for snap_scaffold_3-snap.2731-T1
Valid prediction for snap_scaffold_3-snap.2724-T1
Valid prediction for snap_scaffold_3-snap.2719-T1
Valid prediction for snap_scaffold_3-snap.2697-T1
Valid prediction for Augustus_model.g5086.t1
Valid prediction for snap_scaffold_3-snap.2729-T1
Valid prediction for snap_scaffold_3-snap.2701-T1
Valid prediction for CodingQuarry_transcript_46340-T1
Valid prediction for Augustus_model.g5073.t1
Valid prediction for GlimmerHMM_glimmerT_7699-T1
Valid prediction for GlimmerHMM_glimmerT_7706-T1
Valid prediction for CodingQuarry_transcript_46345-T1
Valid prediction for GlimmerHMM_glimmerT_7733-T1
Valid prediction for snap_scaffold_3-snap.2732-T1
Valid prediction for HiQ_model.g5070.t1
Couldn't classify 7368, 7530
Sorry, prediction pasa_asmbl_39360.p1 fails validation.
(ATG)	 AA	2933-4223	GT	AGG
(GGT)	 AG	4612-4859	GT	ATG
(ACA)	 AG	5063-5144	GT	AAG
(ATA)	 AG	5290-5410	GT	AGG
(TTC)	 AG	5515-5705	GT	AGG
(GGC)	 AG	6056-6195	GT	TGG
(GTG)	 AG	6383-6580	GT	AGG
(GAT)	 AG	6994-7262	GT	CGG
(GGA)	 AG	7368-7530	GT	AGG
-recovered pasa_asmbl_39360.p1, initial, 2933, 4223
-recovered pasa_asmbl_39360.p1, internal, 4612, 4859
-recovered pasa_asmbl_39360.p1, internal, 5063, 5144
-recovered pasa_asmbl_39360.p1, internal, 5290, 5410
-recovered pasa_asmbl_39360.p1, internal, 5515, 5705
-recovered pasa_asmbl_39360.p1, internal, 6056, 6195
-recovered pasa_asmbl_39360.p1, internal, 6383, 6580
-recovered pasa_asmbl_39360.p1, internal, 6994, 7262
-recovered pasa_asmbl_39360.p1, internal, 7368, 7530
Valid prediction for HiQ_model.g5088.t1
Valid prediction for Augustus_model.g5078.t1
Valid prediction for GlimmerHMM_glimmerT_7693-T1
Valid prediction for Augustus_model.g5065.t1
Valid prediction for Augustus_model.g5063.t1
Valid prediction for snap_scaffold_3-snap.2710-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7710-T1
Couldn't classify 177791, 177957
Sorry, prediction pasa_asmbl_39322.p1 fails validation.
(ATG)	 AA	168524-168575	GT	TGG
(TGT)	 AG	168919-169010	GT	TGG
(AAC)	 AG	170390-170576	GT	TGG
(GAA)	 AG	170671-170841	GT	AGG
(GTT)	 AG	170934-171175	GT	GGG
(GAT)	 AG	173854-174012	GT	TGG
(GAC)	 AG	174123-174218	GT	TGG
(GAT)	 AG	174351-174440	GT	ATG
(AAG)	 AG	174562-174699	GT	TGG
(ATT)	 AG	174795-174985	GT	AGG
(TTG)	 AG	175190-175422	GT	AGG
(GTA)	 AG	175794-176013	GT	GGG
(GAA)	 AG	177361-177569	GT	GGG
(AAT)	 AG	177791-177957	GT	AGG
-recovered pasa_asmbl_39322.p1, initial, 168524, 168575
add_exon() Sorry, pasa_asmbl_39322.p1 170671-170841-terminal-1 is invalid.
-recovered pasa_asmbl_39322.p1, terminal, 170671, 170841
-recovered pasa_asmbl_39322.p1, internal, 168919, 169010
-recovered pasa_asmbl_39322.p1, internal, 170390, 170576
-recovered pasa_asmbl_39322.p1, internal, 170671, 170841
-recovered pasa_asmbl_39322.p1, internal, 170934, 171175
-recovered pasa_asmbl_39322.p1, internal, 173854, 174012
-recovered pasa_asmbl_39322.p1, internal, 174123, 174218
-recovered pasa_asmbl_39322.p1, internal, 174351, 174440
-recovered pasa_asmbl_39322.p1, internal, 174562, 174699
-recovered pasa_asmbl_39322.p1, internal, 174795, 174985
-recovered pasa_asmbl_39322.p1, internal, 175190, 175422
-recovered pasa_asmbl_39322.p1, internal, 175794, 176013
-recovered pasa_asmbl_39322.p1, internal, 177361, 177569
-recovered pasa_asmbl_39322.p1, internal, 177791, 177957
Valid prediction for snap_scaffold_3-snap.2722-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7725-T1
Valid prediction for pasa_asmbl_39330.p1
Valid prediction for HiQ_model.g5090.t1
Valid prediction for GlimmerHMM_glimmerT_7718-T1
Valid prediction for snap_scaffold_3-snap.2704-T1
Valid prediction for GlimmerHMM_glimmerT_7719-T1
Valid prediction for GlimmerHMM_glimmerT_7711-T1
Valid prediction for GlimmerHMM_glimmerT_7721-T1
Valid prediction for Augustus_model.g5083.t1
Valid prediction for GlimmerHMM_glimmerT_7728-T1
Valid prediction for GlimmerHMM_glimmerT_7709-T1
Valid prediction for snap_scaffold_3-snap.2707-T1
Couldn't classify 40009, 40089
Couldn't classify 40682, 40805
Sorry, prediction pasa_asmbl_39344.p1 fails validation.
(CAG)	 GG	40009-40089	GT	CGG
(AGC)	 AG	40195-40333	GT	AGG
(GTC)	 AG	40465-40573	GT	CTG
(ACA)	 AG	40682-40805	GA	GTG
-recovered pasa_asmbl_39344.p1, internal, 40195, 40333
-recovered pasa_asmbl_39344.p1, internal, 40465, 40573
Valid prediction for snap_scaffold_3-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_7702-T1
Valid prediction for Augustus_model.g5057.t1
Valid prediction for snap_scaffold_3-snap.2703-T1
Valid prediction for Augustus_model.g5064.t1
Valid prediction for CodingQuarry_transcript_46344-T1
Valid prediction for Augustus_model.g5058.t1
Valid prediction for GlimmerHMM_glimmerT_7696-T1
Valid prediction for GlimmerHMM_glimmerT_7708-T1
Valid prediction for GlimmerHMM_glimmerT_7714-T1
Valid prediction for GlimmerHMM_glimmerT_7723-T1
Valid prediction for Augustus_model.g5068.t1
Valid prediction for Augustus_model.g5075.t1

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

-building trellis in range 1 - 249052
-exon list size: 392


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
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    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
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    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
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    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
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 47 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 45 predictions persist after filtering for low support